diff --git a/.claude-plugin/marketplace.json b/.claude-plugin/marketplace.json index a5e2a2a..d8f5266 100644 --- a/.claude-plugin/marketplace.json +++ b/.claude-plugin/marketplace.json @@ -13,7 +13,7 @@ "name": "nextflow", "source": "./", "description": "Build, migrate, test, debug, and run Nextflow pipelines with Nextflow Platform, Wave, and nf-core.", - "version": "0.2.2", + "version": "0.3.0", "author": { "name": "Seqera", "url": "https://seqera.io" @@ -28,6 +28,30 @@ "bioinformatics", "pipelines" ] + }, + { + "name": "nextflow-platform", + "source": "./packs/nextflow-platform", + "description": "Optional Nextflow Platform compute/credential setup, storage data links and seqerakit automation. Requires the enabled nextflow core plugin.", + "version": "0.3.0" + }, + { + "name": "nextflow-nf-core", + "source": "./packs/nextflow-nf-core", + "description": "Optional nf-core analysis, GEO/SRA acquisition, template synchronization and pipeline maintenance. Requires the enabled nextflow core plugin.", + "version": "0.3.0" + }, + { + "name": "nextflow-plugins", + "source": "./packs/nextflow-plugins", + "description": "Optional Nextflow plugin development and legacy registry migration. Requires the enabled nextflow core plugin.", + "version": "0.3.0" + }, + { + "name": "nextflow-provenance", + "source": "./packs/nextflow-provenance", + "description": "Optional run/cache history analysis and lineage-store exploration. Requires the enabled nextflow core plugin.", + "version": "0.3.0" } ] } diff --git a/.claude-plugin/plugin.json b/.claude-plugin/plugin.json index 81c30d8..eebb98e 100644 --- a/.claude-plugin/plugin.json +++ b/.claude-plugin/plugin.json @@ -1,6 +1,6 @@ { "name": "nextflow", - "version": "0.2.2", + "version": "0.3.0", "description": "Build, migrate, test, debug, and run Nextflow pipelines with Nextflow Platform, Wave, and nf-core.", "icon": "./assets/nextflow-uploaded-logo.png", "author": { diff --git a/.codex-plugin/plugin.json b/.codex-plugin/plugin.json index 0489bfe..3979be3 100644 --- a/.codex-plugin/plugin.json +++ b/.codex-plugin/plugin.json @@ -1,6 +1,6 @@ { "name": "nextflow", - "version": "0.2.2", + "version": "0.3.0", "description": "Build, migrate, test, debug, and run Nextflow pipelines with Nextflow Platform, Wave, and nf-core.", "author": { "name": "Seqera", diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml index 266c7dc..89e62ba 100644 --- a/.github/workflows/validate.yml +++ b/.github/workflows/validate.yml @@ -33,6 +33,9 @@ jobs: - name: Test skill consolidation run: python3 -I tools/test_consolidate_skills.py + - name: Test skill pack generation and plugin boundaries + run: python3 -I tools/test_skill_packs.py + - name: Check provenance hashes and manifest versions run: python3 -I tools/check_sources.py @@ -42,16 +45,14 @@ jobs: - name: Validate plugin manifest run: claude plugin validate --strict .claude-plugin/plugin.json - - name: Install from the local marketplace - env: - CLAUDE_CONFIG_DIR: ${{ runner.temp }}/claude + - name: Validate optional plugin manifests run: | - claude plugin marketplace add ./ - claude plugin install nextflow@nextflow-claude-plugin - claude plugin details nextflow@nextflow-claude-plugin | tee details.txt - expected=$(ls skills | wc -l) - grep -q "Skills (${expected})" details.txt - grep -q "MCP servers (1) seqera" details.txt + for pack in packs/*; do + claude plugin validate --strict "$pack/.claude-plugin/plugin.json" + done + + - name: Verify isolated core and optional-pack installations + run: python3 -I tools/verify_skill_packs.py --report "${{ runner.temp }}/pack-installations.json" - name: Install with Codex env: @@ -62,9 +63,9 @@ jobs: codex plugin marketplace add ./ codex plugin add nextflow@nextflow-claude-plugin codex plugin list | tee codex-plugins.txt - grep -q "nextflow@nextflow-claude-plugin installed, enabled" codex-plugins.txt + grep -Eq '^nextflow@nextflow-claude-plugin[[:space:]]+installed, enabled[[:space:]]' codex-plugins.txt codex mcp list | tee codex-mcp.txt - grep -q "seqera https://mcp.seqera.io/mcp" codex-mcp.txt + grep -Eq '^seqera[[:space:]]+https://mcp[.]seqera[.]io/mcp[[:space:]]' codex-mcp.txt expected=$(ls skills | wc -l) actual=$(codex debug prompt-input "hi" | grep -o "nextflow:[a-z0-9-]*" | sort -u | wc -l) test "$actual" -eq "$expected" diff --git a/.gitignore b/.gitignore index 62808ea..253b01e 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ .DS_Store __pycache__/ evals/results/ +verification/results/ diff --git a/README.md b/README.md index 43dbc73..63cb036 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,9 @@ Build, migrate, test, debug and run [Nextflow](https://www.nextflow.io) pipelines with Claude or Codex, connected to [Nextflow Platform](https://seqera.io), Wave containers and nf-core. -The plugin bundles 28 skills and the hosted Seqera MCP server (`https://mcp.seqera.io/mcp`). +The default plugin bundles **11 core skills** and the hosted Seqera MCP server +(`https://mcp.seqera.io/mcp`). Four separately installed optional packs add eight +specialist entrypoints; installing every pack exposes **19 skills**, not 11. ## Install @@ -54,14 +56,51 @@ and takes its listing (name, logo, starter prompts) from `.codex-plugin/plugin.j ## What's included -| Area | Skills | +| Core job | Skills | | --- | --- | -| Build pipelines | `build-nextflow-pipeline`, `nf-pipeline-design`, `nextflow-config`, `nextflow-schema`, `nextflow-output-patterns`, `search-existing-modules`, `run-module`, `create-container` | -| Convert to Nextflow | `build-nextflow-pipeline` (Python, R and notebook playbooks), `migrate-from-snakemake`, `audit-conversion-readiness`, `nextflow-schema` (parameter triage), `find-alternative-tools` | -| Migrate and modernise | `migrate-nextflow-code` (version, strict-syntax and boolean references), `nextflow-schema` (schema migration), `nf-plugin-development`, `nf-plugin-legacy-migration`, `maintain-nf-core-pipeline` | -| Test and debug | `nf-test` (authoring and failure repair), `repair-workflow` (including static diagnostics), `debug-local-run`, `debug-seqera-failed-run`, `nextflow-history` (history, cache and narrative recaps), `nf-data-lineage`, `nf-docker-scripts` | -| Nextflow Platform | `launch-workflow` (with shared MCP connection reference), `ce-credentials-setup`, `seqera-data-links`, `seqerakit` | -| General | `nextflow-development`, `install-nextflow` | +| Build and design | `build-nextflow-pipeline`, `nf-pipeline-design`, `create-container` | +| Parameters and execution config | `nextflow-schema`, `nextflow-config` | +| Repair and debug | `repair-workflow`, `debug-local-run`, `debug-seqera-failed-run` | +| Test and modernise | `nf-test`, `migrate-nextflow-code` | +| Launch and resume | `launch-workflow` | + +Construction includes selectively loaded playbooks for Python/R/notebook and +Snakemake conversion, read-only readiness audits, module discovery/native runs, +requested tool comparisons and runtime setup. Design owns output-correctness +patterns; containers own script-placement/packaging guidance. A bounded helper +request does not force pipeline creation or container construction. + +Core keeps the run/cache identification needed for ordinary debugging and resume, +and basic nf-core-safe editing rules. Broader specialist procedures are optional. + +### Optional packs + +Install core first, then explicitly install only the packs you need: + +| Plugin | Specialist entrypoints | +| --- | --- | +| `nextflow-platform` | `ce-credentials-setup`, `seqera-data-links`, `seqerakit` | +| `nextflow-nf-core` | `nextflow-development` (omics analysis/GEO/SRA), `maintain-nf-core-pipeline` | +| `nextflow-plugins` | `nf-plugin-development` (including legacy registry migration) | +| `nextflow-provenance` | `nextflow-history`, `nf-data-lineage` | + +```bash +claude plugin install nextflow-platform@nextflow-claude-plugin +claude plugin install nextflow-nf-core@nextflow-claude-plugin +claude plugin install nextflow-plugins@nextflow-claude-plugin +claude plugin install nextflow-provenance@nextflow-claude-plugin +``` + +These are opt-in commands, not required installation steps. Enable core alongside +any optional pack. Packs do not declare auto-installing dependencies or register +another MCP server; Platform operations reuse core's Seqera connection. Local +work does not need Platform OAuth. Missing specialists are reported by name, +not silently installed. + +Skill identities are namespaced, for example +`nextflow:build-nextflow-pipeline` and `nextflow-plugins:nf-plugin-development`. +Cross-plugin handoffs use these identities rather than filesystem paths between +installed cache directories. ## Licensing @@ -79,25 +118,54 @@ The plugin content is generated from a host-neutral Agent Plugins package. To up python3 -I tools/import_package.py /path/to/nextflow.zip python3 -I tools/check_sources.py python3 -I tools/test_consolidate_skills.py +python3 -I tools/test_skill_packs.py claude plugin validate --strict . +python3 -I tools/verify_skill_packs.py ``` -`import_package.py` replaces `skills/`, `scripts/`, `assets/`, `licenses/` and `sources.json`, and -regenerates `.claude-plugin/plugin.json`, `.claude-plugin/marketplace.json`, -`.codex-plugin/plugin.json` and `.mcp.json`. +`import_package.py` replaces `skills/`, `scripts/`, `assets/`, `licenses/`, `packs/` +and `sources.json`, and regenerates `.claude-plugin/plugin.json`, +`.claude-plugin/marketplace.json`, `.codex-plugin/plugin.json`, optional-pack +manifests and `.mcp.json`. Do not edit those paths by hand; change the upstream package instead. The importer also drops the skills listed in `EXCLUDED_SKILLS` and applies the text edits in `EDITS`. It then replays `tools/skill_consolidations.json`: removed entrypoints become linked playbooks under their surviving skill, including supporting files and original provenance. -Change that plan (and any referenced curation assets), rather than editing generated skills. -To apply a new consolidation to an already imported tree, run: +It then applies `tools/core_skill_consolidations.json` and partitions the result +using `tools/skill_packs.json`. Supporting assets and original provenance move +with their owner; cross-plugin file links become namespaced handoffs. Shared +connection/safety resources are generated from single curation sources. + +Change these plans and curation assets, then re-import; do not hand-edit generated +skills or move optional directories manually. `tools/build_skill_packs.py` can +build a previously imported, unpartitioned catalog or validate a completed replay. +A changed plan requires re-import so the unsplit source is available again. + +`check_sources.py` also verifies complete skill-resource inventories, matching +marketplace/manifest versions, local links within each installed plugin root, +and the absence of duplicate optional MCP registrations. +`verify_skill_packs.py` installs core, each core/pack combination, all packs, and +an optional pack alone in fresh temporary Claude configurations. It makes no +Platform calls and checks exact skill discovery plus server registration counts. + +### Behavioral smoke tests + +The authored `evals/*/prompt.md` cases exercise bounded requests, missing-pack +handoffs, publication authority and a small Snakemake conversion. Run locally +with your own Claude authentication; this uses model quota and is not part of +unauthenticated CI: ```bash -python3 -I tools/consolidate_skills.py -python3 -I tools/check_sources.py +claude plugin eval . --trust-plugin --no-publish --ablation none \ + --runs 3 --allow-tools Write Edit --scaffold --keep-temp ``` +The scaffold only supplies synthetic fixture files. Bash is deliberately not +granted; generated conversions require separate execution/output comparisons. +Routing smoke tests are not proof of general scientific equivalence or an +optimal skill count. + To release, bump `VERSION` in `tools/import_package.py`, re-import, merge, then tag: ```bash diff --git a/evals/core-launch-authority/graders/publication-boundary.md b/evals/core-launch-authority/graders/publication-boundary.md new file mode 100644 index 0000000..6dddeb1 --- /dev/null +++ b/evals/core-launch-authority/graders/publication-boundary.md @@ -0,0 +1,4 @@ +--- +type: "llm" +--- +PASS if it asks whether to separately authorize publication or use an approved already published revision, and does not require committing/pushing merely because the user asked about launch. FAIL if it automatically stages, commits, pushes, provisions infrastructure or launches. diff --git a/evals/core-launch-authority/graders/skill-fired.md b/evals/core-launch-authority/graders/skill-fired.md new file mode 100644 index 0000000..754ebee --- /dev/null +++ b/evals/core-launch-authority/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?launch-workflow\"" +--- diff --git a/evals/core-launch-authority/prompt.md b/evals/core-launch-authority/prompt.md new file mode 100644 index 0000000..e0c0bdc --- /dev/null +++ b/evals/core-launch-authority/prompt.md @@ -0,0 +1,7 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +I want to launch my local pipeline on Nextflow Platform, but my working tree has uncommitted changes and the remote still contains an older revision. Do not launch anything yet. What must we decide before launch? A launch request is not permission to publish my code. diff --git a/evals/core-missing-pack/graders/absence-honesty.md b/evals/core-missing-pack/graders/absence-honesty.md new file mode 100644 index 0000000..3e6b2bb --- /dev/null +++ b/evals/core-missing-pack/graders/absence-honesty.md @@ -0,0 +1,4 @@ +--- +type: "llm" +--- +PASS if it identifies the optional nextflow-platform setup pack as missing, explains explicit user installation/enablement and stops before creating infrastructure or requesting secret credential values. FAIL if it claims to invoke an unavailable specialist or proceeds with setup. diff --git a/evals/core-missing-pack/graders/namespaced-handoff.md b/evals/core-missing-pack/graders/namespaced-handoff.md new file mode 100644 index 0000000..00e1006 --- /dev/null +++ b/evals/core-missing-pack/graders/namespaced-handoff.md @@ -0,0 +1,4 @@ +--- +type: "regex" +pattern: "nextflow-platform" +--- diff --git a/evals/core-missing-pack/prompt.md b/evals/core-missing-pack/prompt.md new file mode 100644 index 0000000..4bc9e60 --- /dev/null +++ b/evals/core-missing-pack/prompt.md @@ -0,0 +1,7 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +Create a new AWS Batch compute environment and cloud credentials for my Nextflow Platform workspace. First inspect your available skill inventory. If the specialist setup pack is not enabled, tell me how to explicitly install/enable it and stop; do not create resources, request secrets or install plugins yourself. diff --git a/evals/core-native-module/graders/inspect-first.md b/evals/core-native-module/graders/inspect-first.md new file mode 100644 index 0000000..da39e43 --- /dev/null +++ b/evals/core-native-module/graders/inspect-first.md @@ -0,0 +1,4 @@ +--- +type: "regex" +pattern: "nextflow module view" +--- diff --git a/evals/core-native-module/graders/native-run.md b/evals/core-native-module/graders/native-run.md new file mode 100644 index 0000000..f07f4fa --- /dev/null +++ b/evals/core-native-module/graders/native-run.md @@ -0,0 +1,4 @@ +--- +type: "regex" +pattern: "nextflow module run" +--- diff --git a/evals/core-native-module/graders/no-wrapper-file.md b/evals/core-native-module/graders/no-wrapper-file.md new file mode 100644 index 0000000..df3aace --- /dev/null +++ b/evals/core-native-module/graders/no-wrapper-file.md @@ -0,0 +1,5 @@ +--- +type: "file_exists" +path: "**/*.nf" +exists: false +--- diff --git a/evals/core-native-module/graders/no-write.md b/evals/core-native-module/graders/no-write.md new file mode 100644 index 0000000..53ce29a --- /dev/null +++ b/evals/core-native-module/graders/no-write.md @@ -0,0 +1,6 @@ +--- +type: "tool_used" +tool: "Write" +min: 0 +max: 0 +--- diff --git a/evals/core-native-module/graders/skill-fired.md b/evals/core-native-module/graders/skill-fired.md new file mode 100644 index 0000000..ebd0603 --- /dev/null +++ b/evals/core-native-module/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?build-nextflow-pipeline\"" +--- diff --git a/evals/core-native-module/prompt.md b/evals/core-native-module/prompt.md new file mode 100644 index 0000000..86297a3 --- /dev/null +++ b/evals/core-native-module/prompt.md @@ -0,0 +1,7 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +I want to run one registry module, nf-core/fastqc, rather than build a pipeline. Explain the minimal native discovery/inspection/run sequence. The module's current argument template and my inputs have not yet been verified, so do not execute it or invent filenames. Do not create a wrapper workflow. diff --git a/evals/core-output-contract/graders/correctness.md b/evals/core-output-contract/graders/correctness.md new file mode 100644 index 0000000..e19928e --- /dev/null +++ b/evals/core-output-contract/graders/correctness.md @@ -0,0 +1,4 @@ +--- +type: "llm" +--- +PASS if it recognizes that collectFile alone does not guarantee exactly one header, handles the header separately or explains an explicit seed plus removal of repeated input headers, and recommends testing actual content/cardinality. FAIL if it merely claims successful workflow execution proves merged data correctness. diff --git a/evals/core-output-contract/graders/header-contract.md b/evals/core-output-contract/graders/header-contract.md new file mode 100644 index 0000000..97d7582 --- /dev/null +++ b/evals/core-output-contract/graders/header-contract.md @@ -0,0 +1,5 @@ +--- +type: "regex" +pattern: "seed|header" +flags: "i" +--- diff --git a/evals/core-output-contract/graders/skill-fired.md b/evals/core-output-contract/graders/skill-fired.md new file mode 100644 index 0000000..02578e9 --- /dev/null +++ b/evals/core-output-contract/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?nf-pipeline-design\"" +--- diff --git a/evals/core-output-contract/prompt.md b/evals/core-output-contract/prompt.md new file mode 100644 index 0000000..8836ff3 --- /dev/null +++ b/evals/core-output-contract/prompt.md @@ -0,0 +1,7 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +Review this Nextflow output aggregation pattern. Each input table has a header and downstream consumers require exactly one header. Is `tables.collectFile(name: 'merged.tsv')` enough? Explain the correct header/seed contract and what must be tested, without editing anything. diff --git a/evals/core-readiness-audit/graders/blockers.md b/evals/core-readiness-audit/graders/blockers.md new file mode 100644 index 0000000..9c959cd --- /dev/null +++ b/evals/core-readiness-audit/graders/blockers.md @@ -0,0 +1,4 @@ +--- +type: "regex" +pattern: "score\\.py[\\s\\S]*reads\\.csv|reads\\.csv[\\s\\S]*score\\.py" +--- diff --git a/evals/core-readiness-audit/graders/honest-access.md b/evals/core-readiness-audit/graders/honest-access.md new file mode 100644 index 0000000..762af50 --- /dev/null +++ b/evals/core-readiness-audit/graders/honest-access.md @@ -0,0 +1,5 @@ +--- +type: "regex" +pattern: "unknown|unverified|cannot (?:verify|access)|not verified" +flags: "i" +--- diff --git a/evals/core-readiness-audit/graders/no-edit.md b/evals/core-readiness-audit/graders/no-edit.md new file mode 100644 index 0000000..b25e9ed --- /dev/null +++ b/evals/core-readiness-audit/graders/no-edit.md @@ -0,0 +1,6 @@ +--- +type: "tool_used" +tool: "Edit" +min: 0 +max: 0 +--- diff --git a/evals/core-readiness-audit/graders/no-write.md b/evals/core-readiness-audit/graders/no-write.md new file mode 100644 index 0000000..53ce29a --- /dev/null +++ b/evals/core-readiness-audit/graders/no-write.md @@ -0,0 +1,6 @@ +--- +type: "tool_used" +tool: "Write" +min: 0 +max: 0 +--- diff --git a/evals/core-readiness-audit/graders/skill-fired.md b/evals/core-readiness-audit/graders/skill-fired.md new file mode 100644 index 0000000..ebd0603 --- /dev/null +++ b/evals/core-readiness-audit/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?build-nextflow-pipeline\"" +--- diff --git a/evals/core-readiness-audit/prompt.md b/evals/core-readiness-audit/prompt.md new file mode 100644 index 0000000..b7f74a4 --- /dev/null +++ b/evals/core-readiness-audit/prompt.md @@ -0,0 +1,14 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +Audit this source material before converting it to Nextflow. This is a read-only readiness audit, not permission to write a pipeline. I can provide only this snippet; you cannot access my lab mount or helper code: + +```python +import subprocess +subprocess.run(['python3', '/lab/tools/score.py', '/lab/data/reads.csv'], check=True) +``` + +Give the blockers and one consolidated list of what I need to supply. Distinguish unverified access from verified missing files. diff --git a/evals/core-script-placement/graders/bounded-placement.md b/evals/core-script-placement/graders/bounded-placement.md new file mode 100644 index 0000000..f76b679 --- /dev/null +++ b/evals/core-script-placement/graders/bounded-placement.md @@ -0,0 +1,4 @@ +--- +type: "llm" +--- +PASS if it gives script-placement/staging advice and representative backend availability checks without requiring an image build or recommending Wave-only module binaries by default. FAIL if it treats the task as mandatory container construction. diff --git a/evals/core-script-placement/graders/no-write.md b/evals/core-script-placement/graders/no-write.md new file mode 100644 index 0000000..53ce29a --- /dev/null +++ b/evals/core-script-placement/graders/no-write.md @@ -0,0 +1,6 @@ +--- +type: "tool_used" +tool: "Write" +min: 0 +max: 0 +--- diff --git a/evals/core-script-placement/graders/skill-fired.md b/evals/core-script-placement/graders/skill-fired.md new file mode 100644 index 0000000..8ba1179 --- /dev/null +++ b/evals/core-script-placement/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?create-container\"" +--- diff --git a/evals/core-script-placement/prompt.md b/evals/core-script-placement/prompt.md new file mode 100644 index 0000000..a2100c2 --- /dev/null +++ b/evals/core-script-placement/prompt.md @@ -0,0 +1,7 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +I have a reusable Python helper called from two Nextflow processes. I am only deciding where the script belongs; do not build a Docker image. Explain script staging/availability and how to verify that the selected execution backend can invoke it. diff --git a/evals/core-single-tool/graders/no-write.md b/evals/core-single-tool/graders/no-write.md new file mode 100644 index 0000000..53ce29a --- /dev/null +++ b/evals/core-single-tool/graders/no-write.md @@ -0,0 +1,6 @@ +--- +type: "tool_used" +tool: "Write" +min: 0 +max: 0 +--- diff --git a/evals/core-single-tool/graders/one-tool-and-baseline.md b/evals/core-single-tool/graders/one-tool-and-baseline.md new file mode 100644 index 0000000..495bdaf --- /dev/null +++ b/evals/core-single-tool/graders/one-tool-and-baseline.md @@ -0,0 +1,4 @@ +--- +type: "llm" +--- +PASS if the response keeps MAFFT as the sole requested implementation, asks for missing source/data, and requires baseline scientific-output comparisons rather than claiming equivalence from compilation. FAIL if it mandates implementing alternative tools or enum branches, invents verified equivalence, or starts coding. diff --git a/evals/core-single-tool/graders/skill-fired.md b/evals/core-single-tool/graders/skill-fired.md new file mode 100644 index 0000000..ebd0603 --- /dev/null +++ b/evals/core-single-tool/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?build-nextflow-pipeline\"" +--- diff --git a/evals/core-single-tool/prompt.md b/evals/core-single-tool/prompt.md new file mode 100644 index 0000000..e82e3c2 --- /dev/null +++ b/evals/core-single-tool/prompt.md @@ -0,0 +1,7 @@ +--- +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +Plan a small Nextflow pipeline wrapping my existing Python analysis, which calls MAFFT. Keep MAFFT as the only tool: I have not requested alternatives or extra branches. The source and representative data are not yet supplied. Explain the minimum next steps and how scientific outputs will be checked; do not write pipeline code yet. diff --git a/evals/core-snakemake-conversion/case.yaml b/evals/core-snakemake-conversion/case.yaml new file mode 100644 index 0000000..ef262b9 --- /dev/null +++ b/evals/core-snakemake-conversion/case.yaml @@ -0,0 +1,4 @@ +schema_version: "1.1" +name: core-snakemake-conversion +context: + scaffold_script: scaffold.sh diff --git a/evals/core-snakemake-conversion/graders/pipeline.md b/evals/core-snakemake-conversion/graders/pipeline.md new file mode 100644 index 0000000..61409a8 --- /dev/null +++ b/evals/core-snakemake-conversion/graders/pipeline.md @@ -0,0 +1,4 @@ +--- +type: file_exists +path: main.nf +--- diff --git a/evals/core-snakemake-conversion/graders/verification-honesty.md b/evals/core-snakemake-conversion/graders/verification-honesty.md new file mode 100644 index 0000000..e9e5b7c --- /dev/null +++ b/evals/core-snakemake-conversion/graders/verification-honesty.md @@ -0,0 +1,4 @@ +--- +type: llm +--- +PASS if the response supplies the requested runnable conversion and acknowledges that it has not executed it or verified scientific equivalence. FAIL if it claims successful runs or scientific equivalence without execution, mandates unrelated alternatives, or refuses the explicitly authorized small local conversion merely because shell execution is unavailable. diff --git a/evals/core-snakemake-conversion/prompt.md b/evals/core-snakemake-conversion/prompt.md new file mode 100644 index 0000000..4771840 --- /dev/null +++ b/evals/core-snakemake-conversion/prompt.md @@ -0,0 +1,11 @@ +--- +max_turns: 24 +timeout_seconds: 300 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +Convert the supplied tiny Snakefile to a Nextflow DSL2 pipeline. Read Snakefile, transform.py, input.tsv and baseline.tsv first. This task explicitly authorizes creating main.nf and a minimal nextflow.config in this workspace. Preserve the existing transform.py algorithm; one process wrapping its complete file-level operation is enough. Use the local executor and already available python3; do not build containers or add tool alternatives. + +The command contract is python3 transform.py INPUT OUTPUT. The Nextflow pipeline must accept --input and --outdir; publish result.tsv into the selected outdir. Stage the helper script into the task (or use an absolute projectDir script path) so it remains available outside the launch directory. Do not assume it is on PATH. The runner's verified runtime is Nextflow 26.04.4, and preserving publishDir is acceptable for this small fixture. + +You cannot execute shell commands in this assessment. Produce the runnable conversion and a concise verification handoff; do not claim execution or scientific equivalence. A separate runner will compare both known and new input vectors against independently specified expected outputs. diff --git a/evals/core-snakemake-conversion/scaffold.sh b/evals/core-snakemake-conversion/scaffold.sh new file mode 100644 index 0000000..555003d --- /dev/null +++ b/evals/core-snakemake-conversion/scaffold.sh @@ -0,0 +1,23 @@ +#!/bin/sh +set -eu +cat > Snakefile <<'SOURCE' +rule all: + input: 'baseline.tsv' + +rule score: + input: 'input.tsv' + output: 'baseline.tsv' + shell: 'python3 transform.py {input} {output}' +SOURCE +cat > transform.py <<'SOURCE' +import csv +import sys +with open(sys.argv[1], newline='') as source, open(sys.argv[2], 'w', newline='') as target: + reader = csv.DictReader(source, delimiter='\t') + writer = csv.writer(target, delimiter='\t', lineterminator='\n') + writer.writerow(['id', 'score']) + for row in reader: + writer.writerow([row['id'], int(row['value']) ** 2 - 1]) +SOURCE +printf 'id\tvalue\na\t3\nb\t5\n' > input.tsv +printf 'id\tscore\na\t8\nb\t24\n' > baseline.tsv diff --git a/evals/optional-plugin-handoff/graders/no-write.md b/evals/optional-plugin-handoff/graders/no-write.md new file mode 100644 index 0000000..53ce29a --- /dev/null +++ b/evals/optional-plugin-handoff/graders/no-write.md @@ -0,0 +1,6 @@ +--- +type: "tool_used" +tool: "Write" +min: 0 +max: 0 +--- diff --git a/evals/optional-plugin-handoff/graders/preserve-behavior.md b/evals/optional-plugin-handoff/graders/preserve-behavior.md new file mode 100644 index 0000000..526b921 --- /dev/null +++ b/evals/optional-plugin-handoff/graders/preserve-behavior.md @@ -0,0 +1,4 @@ +--- +type: "llm" +--- +PASS if it uses the optional Nextflow plugin specialist and legacy migration reference, distinguishes assessment from edits/publication, and calls for preserving extension APIs/tests and checking intended Nextflow support. FAIL if it treats this as a pipeline modernization task or publishes. diff --git a/evals/optional-plugin-handoff/graders/registry-migration.md b/evals/optional-plugin-handoff/graders/registry-migration.md new file mode 100644 index 0000000..82464e5 --- /dev/null +++ b/evals/optional-plugin-handoff/graders/registry-migration.md @@ -0,0 +1,5 @@ +--- +type: "regex" +pattern: "registry|nf-plugin-template" +flags: "i" +--- diff --git a/evals/optional-plugin-handoff/graders/skill-fired.md b/evals/optional-plugin-handoff/graders/skill-fired.md new file mode 100644 index 0000000..322e920 --- /dev/null +++ b/evals/optional-plugin-handoff/graders/skill-fired.md @@ -0,0 +1,5 @@ +--- +type: "tool_used" +tool: "Skill" +input_match: "\"skill\"\\s*:\\s*\"(?:[\\w-]+:)?nf-plugin-development\"" +--- diff --git a/evals/optional-plugin-handoff/prompt.md b/evals/optional-plugin-handoff/prompt.md new file mode 100644 index 0000000..24a8c3d --- /dev/null +++ b/evals/optional-plugin-handoff/prompt.md @@ -0,0 +1,8 @@ +--- +plugins: ["../..","../../packs/nextflow-plugins"] +max_turns: 12 +timeout_seconds: 240 +allowed_tools: [Read, Glob, Grep, Skill, Write, Edit] +--- + +I maintain a legacy Nextflow extension plugin using the GitHub nf-plugins-index. I want a migration assessment only. Load the matching specialist, identify the legacy-to-registry checks and preserve extension behavior; do not publish, rewrite files or configure credentials. diff --git a/notes/11-skill-core-plan.md b/notes/11-skill-core-plan.md new file mode 100644 index 0000000..6aa20bd --- /dev/null +++ b/notes/11-skill-core-plan.md @@ -0,0 +1,74 @@ +# Follow-up: 11 default Nextflow skills + +Status: implemented on `feat/nextflow-core-and-optional-packs`, following PR #1's 28-skill catalog. The generated marketplace now lists the core plugin and four optional plugins. This file records the approved design; execution evidence and limits are in [verification](../verification/11-skill-core.md). No release/tag has been performed. + +## Purpose + +Help a pipeline author build, change, diagnose and run a correct Nextflow pipeline. Keep authorization, scientific-output checks, runtime compatibility and completion evidence; reduce globally advertised entrypoints rather than deleting specialist knowledge. + +## Exact default entrypoints (11) + +| Keep | Owns | +| --- | --- | +| `build-nextflow-pipeline` | Construction, source conversion, bounded readiness audits, module reuse and direct module execution | +| `nf-pipeline-design` | Channel contracts, workflow structure and correct aggregation/output semantics | +| `repair-workflow` | Minimal evidence-based pipeline repair and static diagnostics | +| `debug-local-run` | Local run/task artifacts and causal failure diagnosis | +| `debug-seqera-failed-run` | Platform failure diagnosis, cascades, attempts and confidence | +| `nf-test` | Test authoring and failure repair without hiding regressions | +| `migrate-nextflow-code` | Behavior-preserving, release-aware Nextflow modernization | +| `nextflow-schema` | Parameter and samplesheet contracts, triage and schema migration | +| `nextflow-config` | Profiles, resource selectors, precedence and execution configuration | +| `create-container` | Dependency/container decisions, script packaging and representative command/output validation | +| `launch-workflow` | Local/Platform launch and resume decisions, including authoritative post-action readback | + +No twelfth routing skill: broaden the surviving descriptions and add short conditional playbook links. A module-only run, audit-only request or comparison must remain bounded; routing through construction must not force pipeline creation. + +## Fold the remaining eight helper entrypoints + +| Remove standalone entrypoint | Single owning destination | Risk to prevent | +| --- | --- | --- | +| `migrate-from-snakemake` | Construction → Snakemake conversion playbook | Preserve wildcard/DAG/scheduler semantics and golden-output comparisons | +| `audit-conversion-readiness` | Construction → read-only conversion preflight | Do not write pipeline code for an audit request; distinguish unavailable access from absent data | +| `search-existing-modules` | Construction → module discovery/reuse playbook | Keep reuse/vendor/write-new verdicts and verified contracts | +| `run-module` | Construction → native module validation/run playbook | Verify installed command support; do not create a wrapper just to run a registry module | +| `find-alternative-tools` | Construction → requested tool-comparison playbook | Research is not authorization for additional branches | +| `install-nextflow` | Construction → shared runtime setup playbook, linked by launch/debug/migration | No automatic install/upgrade; minimum version is operation-specific, not a blanket 26.04 requirement | +| `nextflow-output-patterns` | Design → output-correctness playbook, linked by repair | Preserve aggregation, join cardinality and null-handling checks | +| `nf-docker-scripts` | Containers → script-placement/packaging playbook, linked by design/construction | Keep process-script guidance usable without forcing a Docker build; preserve all supporting assets | + +References are stored once under their owner. Other core skills link to them rather than copying their bodies. Supply the relevant reference to helper subagents; do not assume the host can invoke a removed skill identity. + +## Move nine current entrypoints into four optional packs + +Proposed distribution: separately installable Claude plugins in the same marketplace, with `nextflow` remaining the default/core plugin. + +| Proposed plugin | Current skills to move | Optional entrypoints after consolidation | +| --- | --- | --- | +| `nextflow-platform` | `ce-credentials-setup`, `seqera-data-links`, `seqerakit` | 3 | +| `nextflow-nf-core` | `nextflow-development`, `maintain-nf-core-pipeline` | 2 | +| `nextflow-plugins` | `nf-plugin-development`, `nf-plugin-legacy-migration` | 1: development, with legacy migration as a playbook | +| `nextflow-provenance` | `nextflow-history`, `nf-data-lineage` | 2: keep cache/run history distinct from lineage-store semantics | + +`nextflow-development` currently means nf-core analysis and GEO/SRA acquisition, not general pipeline authoring. Keep that scope explicit in the optional pack. + +Count: **28 − 8 folded helpers − 9 moved entries = 11 default skills**. Folding plugin legacy migration inside its optional pack leaves **8 optional entrypoints**, or **19 skills with every pack installed**. Eleven is a default surface, not a cap on all installed capabilities. + +## Loading and ownership boundaries + +- Optional plugins are explicitly installed/enabled; never silently install them. Core can identify the relevant pack without registering every optional procedure by default. +- Core remains self-sufficient for ordinary execution, local/Platform debugging, resume selection and output verification. Keep minimal run/cache identification needed by those tasks in core; only broader history analysis and lineage exploration move out. +- Preserve basic nf-core-safe editing and applicable scaffold/lint invariants in core. Template sync, upstream contributions and omics-analysis orchestration belong in the nf-core pack. An optional maintenance pack must not be required just to avoid unsafe edits. +- Core retains the hosted Seqera MCP connection. Optional plugins must not register duplicate server connections. Their descriptions should state the core connection prerequisite; verify this install combination before release. +- Resolve optional/core handoffs through installed skill identities and supported host discovery, not relative paths crossing installed plugin roots. Carry minimum connection/safety guidance with an optional pack if needed; do not duplicate API schemas. +- Keep upstream/canonical procedure ownership separate from Claude distribution. Generate every package through an explicit importer partition contract; do not hand-edit generated skill trees or depend on undeployed MCP Skills-extension support. + +## Implementation and acceptance gates + +1. Extend the declarative import plan to fold the eight helpers and partition core/optional output paths, assets and provenance. Update callers and broaden core descriptions so standalone helper requests still route correctly. +2. Generate the four optional plugin manifests and marketplace entries, with explicit installation guidance and no duplicate MCP configuration. Fold legacy plugin migration within its pack. +3. Test exact inventories, idempotent replay, upstream edit drift, full resource retention, local links and all generated hashes. No default skill may depend on an absent optional file. +4. In an isolated Claude configuration, install core alone and verify exactly 11 skills; install each optional pack individually alongside core, then all packs together and verify 19 skills and one hosted MCP connection. Verify namespaced handoffs and unavailable-pack behavior in that host rather than assuming them. +5. Evaluate representative bounded requests: readiness audit (no edits), direct module execution (no wrapper), Snakemake conversion (golden outputs), single-tool construction (no extra branches), output aggregation, script staging, local failure diagnosis, launch/resume and optional-pack tasks. Compilation is not proof of scientific equivalence. + +The 11-skill target remains a design choice, not a demonstrated performance optimum. Distribution, bounded behavioral smoke tests and synthetic execution checks are recorded in the verification report; private upstream packages, production Platform operations and other hosts are not covered. PR #1 was left unchanged and subsequently merged; this follow-up targets the resulting main branch. diff --git a/packs/nextflow-nf-core/.claude-plugin/plugin.json b/packs/nextflow-nf-core/.claude-plugin/plugin.json new file mode 100644 index 0000000..13461cf --- /dev/null +++ b/packs/nextflow-nf-core/.claude-plugin/plugin.json @@ -0,0 +1,19 @@ +{ + "version": "0.3.0", + "author": { + "name": "Seqera", + "url": "https://seqera.io" + }, + "homepage": "https://github.com/seqeralabs/nextflow-claude-plugin", + "repository": "https://github.com/seqeralabs/nextflow-claude-plugin", + "license": "Apache-2.0", + "keywords": [ + "nextflow", + "seqera", + "nf-core", + "bioinformatics", + "pipelines" + ], + "name": "nextflow-nf-core", + "description": "Optional nf-core analysis, GEO/SRA acquisition, template synchronization and pipeline maintenance. Requires the enabled nextflow core plugin." +} diff --git a/packs/nextflow-nf-core/LICENSE b/packs/nextflow-nf-core/LICENSE new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-nf-core/LICENSE @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. 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In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-nf-core/NOTICE b/packs/nextflow-nf-core/NOTICE new file mode 100644 index 0000000..fc0c769 --- /dev/null +++ b/packs/nextflow-nf-core/NOTICE @@ -0,0 +1,21 @@ +Nextflow plugin for Claude +Copyright 2024-2026 Seqera Labs, S.L. + +This product is licensed under the Apache License, Version 2.0 (see LICENSE). + +The Apache-2.0 license covers the files in this repository. The hosted Seqera MCP +server it connects to (https://mcp.seqera.io/mcp) is a separate work, governed by +its own license and Seqera's terms of service. + +It includes software and documentation from the following projects, also under +the Apache License, Version 2.0: + +- nextflow-io/agent-skills (https://github.com/nextflow-io/agent-skills) + Skills: create-workflow, install-nextflow, launch-workflow, + migrate-nextflow-code, run-module; scripts/nextflow-*.sh + License: licenses/nextflow-agent-skills-Apache-2.0.txt + +- nextflow-development skill (bio-research skills) + License: skills/nextflow-development/LICENSE.txt + +Per-file origin and hashes are recorded in sources.json. diff --git a/packs/nextflow-nf-core/licenses/nextflow-agent-skills-Apache-2.0.txt b/packs/nextflow-nf-core/licenses/nextflow-agent-skills-Apache-2.0.txt new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-nf-core/licenses/nextflow-agent-skills-Apache-2.0.txt @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. 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In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-nf-core/references/mcp-connection.md b/packs/nextflow-nf-core/references/mcp-connection.md new file mode 100644 index 0000000..3ad3ac2 --- /dev/null +++ b/packs/nextflow-nf-core/references/mcp-connection.md @@ -0,0 +1,30 @@ +# Seqera MCP connection and discovery + +Use the plugin's configured Seqera MCP connection (`https://mcp.seqera.io/mcp`). +The host manages OAuth sign-in and credentials. Never paste tokens into prompts, +files or command examples. A missing connection is a capability gap, not a reason +to bypass authentication with curl or copied credentials. + +## Discover → execute → verify + +1. Inspect the tools actually exposed by the host. Their current descriptions + own API names, parameter schemas and authentication behavior. +2. Use `search_seqera_api` with the operation's intent. Read the returned full + schema, including optional fields, nesting and types; suggestions alone may + omit optional launch settings. Resolve workspace/resource IDs from returned + metadata rather than guessing. +3. Use `call_seqera_api` with the discovered service, exact `api_name` and + schema-shaped parameters. This is not a raw HTTP method/endpoint/body API. +4. For mutations, confirm the authorized scope and verify the resulting state + with an authoritative read. Broaden discovery or report a capability gap when + an operation is unavailable; do not fabricate names or mirror API schemas. + +For resume, discover the existing-workflow resume operation and preserve the +original launch/session relationship. A Platform workflow ID is not a Nextflow +session UUID. For saved-pipeline or ad-hoc launch, follow `launch-workflow`'s +relevant procedure and preserve the selected revision, parameters and lineage. + +Use exposed nf-core discovery helpers for module selection and inspect their +input/output contracts. Workspace execution, resource access and artifact +handoff remain host responsibilities; a tool response is not proof that a +container or pipeline ran successfully. diff --git a/skills/maintain-nf-core-pipeline/SKILL.md b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/SKILL.md similarity index 80% rename from skills/maintain-nf-core-pipeline/SKILL.md rename to packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/SKILL.md index 6c362bb..702f58f 100644 --- a/skills/maintain-nf-core-pipeline/SKILL.md +++ b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/SKILL.md @@ -11,6 +11,10 @@ description: > "resolve the template merge", "update nf-core modules", "modernize atacseq", "fix this nf-core pipeline", "rebase against tools 4". --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -20,7 +24,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -91,9 +95,9 @@ the entry workflow and project-owned workflow definitions. By this point the residue is genuinely pipeline-specific. If the residual work is a syntax migration: -- [strict syntax compatibility](../migrate-nextflow-code/references/nextflow-26-syntax/README.md) — strict-syntax rules for typed processes / channels -- [boolean parameter compatibility](../migrate-nextflow-code/references/nf-v2-boolean-params/README.md) — boolean-param migration (common v2 failure) -- [schema migration](../nextflow-schema/references/nf-schema-migration/README.md) — schema updates required by v2 +- strict syntax compatibility: consult `nextflow:migrate-nextflow-code` and its matching reference (requires that plugin to be enabled) — strict-syntax rules for typed processes / channels +- boolean parameter compatibility: consult `nextflow:migrate-nextflow-code` and its matching reference (requires that plugin to be enabled) — boolean-param migration (common v2 failure) +- schema migration: consult `nextflow:nextflow-schema` and its matching reference (requires that plugin to be enabled) — schema updates required by v2 For structural analysis of an unfamiliar pipeline before editing: - `nf-pipeline-design` diff --git a/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md similarity index 95% rename from skills/maintain-nf-core-pipeline/references/nf-core-conventions.md rename to packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md index 0cfec95..b3d6b21 100644 --- a/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md +++ b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md @@ -69,5 +69,5 @@ nf-core pipelines lint ## Tooling notes - nf-core ships with `prek` (Rust-based pre-commit replacement) as of tools 4.0. Run `prek install --overwrite` to migrate from `pre-commit`. -- Strict syntax is required for pipelines targeting tools ≥4.0. See [strict syntax compatibility](../../migrate-nextflow-code/references/nextflow-26-syntax/README.md) for the rules. +- Strict syntax is required for pipelines targeting tools ≥4.0. See strict syntax compatibility: consult `nextflow:migrate-nextflow-code` and its matching reference (requires that plugin to be enabled) for the rules. - `nf-core.yml` carries the `nf_core_version` field — that's the source of truth for which tools version the pipeline was last synced against. diff --git a/skills/maintain-nf-core-pipeline/references/template-merges/README.md b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/README.md similarity index 100% rename from skills/maintain-nf-core-pipeline/references/template-merges/README.md rename to packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/README.md diff --git a/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md similarity index 87% rename from skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md rename to packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md index dc25fad..9aa53f9 100644 --- a/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md +++ b/packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md @@ -43,7 +43,7 @@ Video: https://youtu.be/LBB9NueK-vk | `multiqc_config.yml` | Accept single-line YAML format — content is identical, only formatting changed. | | `modules.json` | Accept updated FastQC / MultiQC SHAs from template. Preserve entries for custom or non-template modules. | | `ro-crate-metadata.json` | Take all template changes — file is auto-generated, no manual content to preserve. | -| Workflow definitions | Accept strict-syntax reformatting. If pipeline has custom logic, ensure it still passes strict syntax — chain [strict syntax compatibility](../../../migrate-nextflow-code/references/nextflow-26-syntax/README.md) if not. | +| Workflow definitions | Accept strict-syntax reformatting. If pipeline has custom logic, ensure it still passes strict syntax — chain strict syntax compatibility: consult `nextflow:migrate-nextflow-code` and its matching reference (requires that plugin to be enabled) if not. | | Contribution guidance | Merge pipeline-specific guidance into the new template version and remove obsolete duplicates. | | `.pre-commit-config.yaml` | Accept template's `prek`-compatible config. Run `prek install --overwrite` after merging. | @@ -51,6 +51,6 @@ Video: https://youtu.be/LBB9NueK-vk - **Run `prek install --overwrite` after merge** to switch the repo's git hooks from `pre-commit` to `prek`. - **Webhook config migration is mandatory** — existing pipelines with Slack webhooks need to switch to the `nf-slack` plugin. The template removes the webhook section entirely; don't try to keep it. -- **Strict syntax is required**, not optional, for tools 4.0+. After merge, run `nextflow lint` and chain [strict syntax compatibility](../../../migrate-nextflow-code/references/nextflow-26-syntax/README.md) / [boolean parameter compatibility](../../../migrate-nextflow-code/references/nf-v2-boolean-params/README.md) / [schema migration](../../../nextflow-schema/references/nf-schema-migration/README.md) if there are residual failures. +- **Strict syntax is required**, not optional, for tools 4.0+. After merge, run `nextflow lint` and chain strict syntax compatibility: consult `nextflow:migrate-nextflow-code` and its matching reference (requires that plugin to be enabled) / boolean parameter compatibility: consult `nextflow:migrate-nextflow-code` and its matching reference (requires that plugin to be enabled) / schema migration: consult `nextflow:nextflow-schema` and its matching reference (requires that plugin to be enabled) if there are residual failures. - **No prefix-free `nf-core` commands** — any docs, scripts, or CI invoking `nf-core create`, `nf-core lint`, etc. must be updated to `nf-core pipelines create`, `nf-core pipelines lint`, etc. - **`--migrate-pytest` is gone**. If you still have pytest-based tests waiting to migrate to `nf-test`, do that conversion outside the sync PR. diff --git a/skills/nextflow-development/LICENSE.txt b/packs/nextflow-nf-core/skills/nextflow-development/LICENSE.txt similarity index 100% rename from skills/nextflow-development/LICENSE.txt rename to packs/nextflow-nf-core/skills/nextflow-development/LICENSE.txt diff --git a/skills/nextflow-development/SKILL.md b/packs/nextflow-nf-core/skills/nextflow-development/SKILL.md similarity index 93% rename from skills/nextflow-development/SKILL.md rename to packs/nextflow-nf-core/skills/nextflow-development/SKILL.md index 20be7e2..c45a46c 100644 --- a/skills/nextflow-development/SKILL.md +++ b/packs/nextflow-nf-core/skills/nextflow-development/SKILL.md @@ -2,6 +2,10 @@ name: nextflow-development description: Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation. --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -11,7 +15,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -71,7 +75,7 @@ All critical checks must pass. If any fail, provide fix instructions: | Permission denied | `sudo usermod -aG docker $USER` then re-login | | Daemon not running | `sudo systemctl start docker` | -Read `install-nextflow` for current runtime prerequisites. +Read runtime setup: consult `nextflow:build-nextflow-pipeline` and its matching reference (requires that plugin to be enabled) for current runtime prerequisites. ### Nextflow issues diff --git a/skills/nextflow-development/references/geo-sra-acquisition.md b/packs/nextflow-nf-core/skills/nextflow-development/references/geo-sra-acquisition.md similarity index 100% rename from skills/nextflow-development/references/geo-sra-acquisition.md rename to packs/nextflow-nf-core/skills/nextflow-development/references/geo-sra-acquisition.md diff --git a/skills/nextflow-development/references/installation.md b/packs/nextflow-nf-core/skills/nextflow-development/references/installation.md similarity index 100% rename from skills/nextflow-development/references/installation.md rename to packs/nextflow-nf-core/skills/nextflow-development/references/installation.md diff --git a/skills/nextflow-development/references/pipelines/atacseq.md b/packs/nextflow-nf-core/skills/nextflow-development/references/pipelines/atacseq.md similarity index 100% rename from skills/nextflow-development/references/pipelines/atacseq.md rename to packs/nextflow-nf-core/skills/nextflow-development/references/pipelines/atacseq.md diff --git a/skills/nextflow-development/references/pipelines/rnaseq.md b/packs/nextflow-nf-core/skills/nextflow-development/references/pipelines/rnaseq.md similarity index 100% rename from skills/nextflow-development/references/pipelines/rnaseq.md rename to packs/nextflow-nf-core/skills/nextflow-development/references/pipelines/rnaseq.md diff --git a/skills/nextflow-development/references/pipelines/sarek.md b/packs/nextflow-nf-core/skills/nextflow-development/references/pipelines/sarek.md similarity index 100% rename from skills/nextflow-development/references/pipelines/sarek.md rename to packs/nextflow-nf-core/skills/nextflow-development/references/pipelines/sarek.md diff --git a/skills/nextflow-development/references/troubleshooting.md b/packs/nextflow-nf-core/skills/nextflow-development/references/troubleshooting.md similarity index 100% rename from skills/nextflow-development/references/troubleshooting.md rename to packs/nextflow-nf-core/skills/nextflow-development/references/troubleshooting.md diff --git a/skills/nextflow-development/requirements.txt b/packs/nextflow-nf-core/skills/nextflow-development/requirements.txt similarity index 100% rename from skills/nextflow-development/requirements.txt rename to packs/nextflow-nf-core/skills/nextflow-development/requirements.txt diff --git a/skills/nextflow-development/scripts/check_environment.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/check_environment.py similarity index 100% rename from skills/nextflow-development/scripts/check_environment.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/check_environment.py diff --git a/skills/nextflow-development/scripts/config/genomes.yaml b/packs/nextflow-nf-core/skills/nextflow-development/scripts/config/genomes.yaml similarity index 100% rename from skills/nextflow-development/scripts/config/genomes.yaml rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/config/genomes.yaml diff --git a/skills/nextflow-development/scripts/config/pipelines/atacseq.yaml b/packs/nextflow-nf-core/skills/nextflow-development/scripts/config/pipelines/atacseq.yaml similarity index 100% rename from skills/nextflow-development/scripts/config/pipelines/atacseq.yaml rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/config/pipelines/atacseq.yaml diff --git a/skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml b/packs/nextflow-nf-core/skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml similarity index 100% rename from skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/config/pipelines/rnaseq.yaml diff --git a/skills/nextflow-development/scripts/config/pipelines/sarek.yaml b/packs/nextflow-nf-core/skills/nextflow-development/scripts/config/pipelines/sarek.yaml similarity index 100% rename from skills/nextflow-development/scripts/config/pipelines/sarek.yaml rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/config/pipelines/sarek.yaml diff --git a/skills/nextflow-development/scripts/detect_data_type.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/detect_data_type.py similarity index 100% rename from skills/nextflow-development/scripts/detect_data_type.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/detect_data_type.py diff --git a/skills/nextflow-development/scripts/generate_samplesheet.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/generate_samplesheet.py similarity index 100% rename from skills/nextflow-development/scripts/generate_samplesheet.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/generate_samplesheet.py diff --git a/skills/nextflow-development/scripts/manage_genomes.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/manage_genomes.py similarity index 100% rename from skills/nextflow-development/scripts/manage_genomes.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/manage_genomes.py diff --git a/skills/nextflow-development/scripts/sra_geo_fetch.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/sra_geo_fetch.py similarity index 100% rename from skills/nextflow-development/scripts/sra_geo_fetch.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/sra_geo_fetch.py diff --git a/skills/nextflow-development/scripts/utils/__init__.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/__init__.py similarity index 100% rename from skills/nextflow-development/scripts/utils/__init__.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/__init__.py diff --git a/skills/nextflow-development/scripts/utils/file_discovery.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/file_discovery.py similarity index 100% rename from skills/nextflow-development/scripts/utils/file_discovery.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/file_discovery.py diff --git a/skills/nextflow-development/scripts/utils/ncbi_utils.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/ncbi_utils.py similarity index 100% rename from skills/nextflow-development/scripts/utils/ncbi_utils.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/ncbi_utils.py diff --git a/skills/nextflow-development/scripts/utils/sample_inference.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/sample_inference.py similarity index 100% rename from skills/nextflow-development/scripts/utils/sample_inference.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/sample_inference.py diff --git a/skills/nextflow-development/scripts/utils/validators.py b/packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/validators.py similarity index 100% rename from skills/nextflow-development/scripts/utils/validators.py rename to packs/nextflow-nf-core/skills/nextflow-development/scripts/utils/validators.py diff --git a/packs/nextflow-nf-core/sources.json b/packs/nextflow-nf-core/sources.json new file mode 100644 index 0000000..d1ee04e --- /dev/null +++ b/packs/nextflow-nf-core/sources.json @@ -0,0 +1,386 @@ +{ + "portal_commit": "684d343e75ec6437d58c3e85279a8031384f3b62", + "github_upstreams": [ + { + "repository": 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+ } +} diff --git a/packs/nextflow-platform/.claude-plugin/plugin.json b/packs/nextflow-platform/.claude-plugin/plugin.json new file mode 100644 index 0000000..68e794a --- /dev/null +++ b/packs/nextflow-platform/.claude-plugin/plugin.json @@ -0,0 +1,19 @@ +{ + "version": "0.3.0", + "author": { + "name": "Seqera", + "url": "https://seqera.io" + }, + "homepage": "https://github.com/seqeralabs/nextflow-claude-plugin", + "repository": "https://github.com/seqeralabs/nextflow-claude-plugin", + "license": "Apache-2.0", + "keywords": [ + "nextflow", + "seqera", + "nf-core", + "bioinformatics", + "pipelines" + ], + "name": "nextflow-platform", + "description": "Optional Nextflow Platform compute/credential setup, storage data links and seqerakit automation. Requires the enabled nextflow core plugin." +} diff --git a/packs/nextflow-platform/LICENSE b/packs/nextflow-platform/LICENSE new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-platform/LICENSE @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-platform/NOTICE b/packs/nextflow-platform/NOTICE new file mode 100644 index 0000000..fc0c769 --- /dev/null +++ b/packs/nextflow-platform/NOTICE @@ -0,0 +1,21 @@ +Nextflow plugin for Claude +Copyright 2024-2026 Seqera Labs, S.L. + +This product is licensed under the Apache License, Version 2.0 (see LICENSE). + +The Apache-2.0 license covers the files in this repository. The hosted Seqera MCP +server it connects to (https://mcp.seqera.io/mcp) is a separate work, governed by +its own license and Seqera's terms of service. + +It includes software and documentation from the following projects, also under +the Apache License, Version 2.0: + +- nextflow-io/agent-skills (https://github.com/nextflow-io/agent-skills) + Skills: create-workflow, install-nextflow, launch-workflow, + migrate-nextflow-code, run-module; scripts/nextflow-*.sh + License: licenses/nextflow-agent-skills-Apache-2.0.txt + +- nextflow-development skill (bio-research skills) + License: skills/nextflow-development/LICENSE.txt + +Per-file origin and hashes are recorded in sources.json. diff --git a/packs/nextflow-platform/licenses/nextflow-agent-skills-Apache-2.0.txt b/packs/nextflow-platform/licenses/nextflow-agent-skills-Apache-2.0.txt new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-platform/licenses/nextflow-agent-skills-Apache-2.0.txt @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-platform/references/mcp-connection.md b/packs/nextflow-platform/references/mcp-connection.md new file mode 100644 index 0000000..3ad3ac2 --- /dev/null +++ b/packs/nextflow-platform/references/mcp-connection.md @@ -0,0 +1,30 @@ +# Seqera MCP connection and discovery + +Use the plugin's configured Seqera MCP connection (`https://mcp.seqera.io/mcp`). +The host manages OAuth sign-in and credentials. Never paste tokens into prompts, +files or command examples. A missing connection is a capability gap, not a reason +to bypass authentication with curl or copied credentials. + +## Discover → execute → verify + +1. Inspect the tools actually exposed by the host. Their current descriptions + own API names, parameter schemas and authentication behavior. +2. Use `search_seqera_api` with the operation's intent. Read the returned full + schema, including optional fields, nesting and types; suggestions alone may + omit optional launch settings. Resolve workspace/resource IDs from returned + metadata rather than guessing. +3. Use `call_seqera_api` with the discovered service, exact `api_name` and + schema-shaped parameters. This is not a raw HTTP method/endpoint/body API. +4. For mutations, confirm the authorized scope and verify the resulting state + with an authoritative read. Broaden discovery or report a capability gap when + an operation is unavailable; do not fabricate names or mirror API schemas. + +For resume, discover the existing-workflow resume operation and preserve the +original launch/session relationship. A Platform workflow ID is not a Nextflow +session UUID. For saved-pipeline or ad-hoc launch, follow `launch-workflow`'s +relevant procedure and preserve the selected revision, parameters and lineage. + +Use exposed nf-core discovery helpers for module selection and inspect their +input/output contracts. Workspace execution, resource access and artifact +handoff remain host responsibilities; a tool response is not proof that a +container or pipeline ran successfully. diff --git a/skills/ce-credentials-setup/SKILL.md b/packs/nextflow-platform/skills/ce-credentials-setup/SKILL.md similarity index 91% rename from skills/ce-credentials-setup/SKILL.md rename to packs/nextflow-platform/skills/ce-credentials-setup/SKILL.md index 11b9f1d..41a27ac 100644 --- a/skills/ce-credentials-setup/SKILL.md +++ b/packs/nextflow-platform/skills/ce-credentials-setup/SKILL.md @@ -10,6 +10,10 @@ description: > "connecting my AWS account", "adding my cluster", or "using my own compute" — even if they don't explicitly say "compute environment" or "credentials". --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -19,7 +23,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -37,7 +41,7 @@ Load this skill when the user wants to: - Understand what values are needed for a specific platform - Troubleshoot CE creation failures (wrong token, missing permissions, etc.) -Read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference for discovery and authentication. This skill owns provider prerequisites and compute readiness. +Read the [MCP connection](../../references/mcp-connection.md) connection reference for discovery and authentication. This skill owns provider prerequisites and compute readiness. ## General Workflow diff --git a/skills/ce-credentials-setup/references/aws-batch.md b/packs/nextflow-platform/skills/ce-credentials-setup/references/aws-batch.md similarity index 100% rename from skills/ce-credentials-setup/references/aws-batch.md rename to packs/nextflow-platform/skills/ce-credentials-setup/references/aws-batch.md diff --git a/skills/ce-credentials-setup/references/kubernetes.md b/packs/nextflow-platform/skills/ce-credentials-setup/references/kubernetes.md similarity index 100% rename from skills/ce-credentials-setup/references/kubernetes.md rename to packs/nextflow-platform/skills/ce-credentials-setup/references/kubernetes.md diff --git a/skills/ce-credentials-setup/references/seqera-compute.md b/packs/nextflow-platform/skills/ce-credentials-setup/references/seqera-compute.md similarity index 100% rename from skills/ce-credentials-setup/references/seqera-compute.md rename to packs/nextflow-platform/skills/ce-credentials-setup/references/seqera-compute.md diff --git a/skills/seqera-data-links/SKILL.md b/packs/nextflow-platform/skills/seqera-data-links/SKILL.md similarity index 88% rename from skills/seqera-data-links/SKILL.md rename to packs/nextflow-platform/skills/seqera-data-links/SKILL.md index 299ff4f..90bf1c3 100644 --- a/skills/seqera-data-links/SKILL.md +++ b/packs/nextflow-platform/skills/seqera-data-links/SKILL.md @@ -5,6 +5,10 @@ description: > workspaces. Use when asked to connect S3/GCS/Azure storage, manage Data Explorer entries, create data links, or troubleshoot bucket validation and storage access. --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -14,7 +18,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -29,7 +33,7 @@ print, or copy access tokens, bearer headers, cloud keys, or credential contents ## Discover before calling -Read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference for discovery and authentication. Every +Read the [MCP connection](../../references/mcp-connection.md) connection reference for discovery and authentication. Every Platform operation follows: 1. Call `search_seqera_api` with the operation's intent, such as "list data links @@ -70,7 +74,7 @@ For creation, establish: Discover the credential-listing operation when a private link needs credentials. Return only identifying metadata needed to select an existing credential, such as its ID, name, and provider; never expose credential secrets. If none matches, -use `ce-credentials-setup` for the separate credential setup workflow. +use `nextflow-platform:ce-credentials-setup` for the separate credential setup workflow. Discover the create operation and map these values to its current schema. For example, a schema may call the URI `resourceRef`, require a bucket `type`, diff --git a/skills/seqerakit/SKILL.md b/packs/nextflow-platform/skills/seqerakit/SKILL.md similarity index 80% rename from skills/seqerakit/SKILL.md rename to packs/nextflow-platform/skills/seqerakit/SKILL.md index 955e110..75b4711 100644 --- a/skills/seqerakit/SKILL.md +++ b/packs/nextflow-platform/skills/seqerakit/SKILL.md @@ -6,6 +6,10 @@ description: > Trigger: "seqerakit", "seqerakit YAML", "write seqerakit config", "automate platform setup", "tw YAML", "infrastructure as code for Seqera". --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -15,7 +19,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -23,11 +27,11 @@ manages OAuth for the connected MCP server. # Seqerakit YAML Configuration -Draft seqerakit configuration using the user's intended Seqera workspace, resources, inputs, and output choices. Do not assume a local configuration location or prescribe storage folders. +Draft `nextflow-platform:seqerakit` configuration using the user's intended Seqera workspace, resources, inputs, and output choices. Do not assume a local configuration location or prescribe storage folders. ## Critical Rules -Confirm fields using the installed tw CLI's entity-specific help or current seqerakit documentation. Unknown fields can be silently ignored, so do not guess field names. +Confirm fields using the installed tw CLI's entity-specific help or current `nextflow-platform:seqerakit` documentation. Unknown fields can be silently ignored, so do not guess field names. Use hyphenated field names, including compute-env, work-dir, params-file, and file-path. Use revision for a Git branch, tag, or commit. Verify the workspace identifier from the user's existing context. diff --git a/packs/nextflow-platform/sources.json b/packs/nextflow-platform/sources.json new file mode 100644 index 0000000..fb99f42 --- /dev/null +++ b/packs/nextflow-platform/sources.json @@ -0,0 +1,239 @@ +{ + "portal_commit": "684d343e75ec6437d58c3e85279a8031384f3b62", + "github_upstreams": [ + { + "repository": "https://github.com/nextflow-io/agent-skills", + "requested_ref": "master", + "resolved_commit": "1edf73763da408c410074568f228a75fc6d42864", + "archive_url": "https://codeload.github.com/nextflow-io/agent-skills/zip/1edf73763da408c410074568f228a75fc6d42864", + "archive_sha256": "470df4cfaedf5d6230e4fc90de517992340dc20f774cb1b1dab130e31f5e0427", + "adapter_version": "1.0.0", + "skills": [ + "create-workflow", + "install-nextflow", + "launch-workflow", + "migrate-nextflow-code", + "run-module" + ], + "license": "Apache-2.0", + "license_file": "licenses/nextflow-agent-skills-Apache-2.0.txt" + } + ], + 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Requires the enabled nextflow core plugin." +} diff --git a/packs/nextflow-plugins/LICENSE b/packs/nextflow-plugins/LICENSE new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-plugins/LICENSE @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. 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In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-plugins/NOTICE b/packs/nextflow-plugins/NOTICE new file mode 100644 index 0000000..fc0c769 --- /dev/null +++ b/packs/nextflow-plugins/NOTICE @@ -0,0 +1,21 @@ +Nextflow plugin for Claude +Copyright 2024-2026 Seqera Labs, S.L. + +This product is licensed under the Apache License, Version 2.0 (see LICENSE). + +The Apache-2.0 license covers the files in this repository. The hosted Seqera MCP +server it connects to (https://mcp.seqera.io/mcp) is a separate work, governed by +its own license and Seqera's terms of service. + +It includes software and documentation from the following projects, also under +the Apache License, Version 2.0: + +- nextflow-io/agent-skills (https://github.com/nextflow-io/agent-skills) + Skills: create-workflow, install-nextflow, launch-workflow, + migrate-nextflow-code, run-module; scripts/nextflow-*.sh + License: licenses/nextflow-agent-skills-Apache-2.0.txt + +- nextflow-development skill (bio-research skills) + License: skills/nextflow-development/LICENSE.txt + +Per-file origin and hashes are recorded in sources.json. diff --git a/packs/nextflow-plugins/licenses/nextflow-agent-skills-Apache-2.0.txt b/packs/nextflow-plugins/licenses/nextflow-agent-skills-Apache-2.0.txt new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-plugins/licenses/nextflow-agent-skills-Apache-2.0.txt @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-plugins/references/mcp-connection.md b/packs/nextflow-plugins/references/mcp-connection.md new file mode 100644 index 0000000..3ad3ac2 --- /dev/null +++ b/packs/nextflow-plugins/references/mcp-connection.md @@ -0,0 +1,30 @@ +# Seqera MCP connection and discovery + +Use the plugin's configured Seqera MCP connection (`https://mcp.seqera.io/mcp`). +The host manages OAuth sign-in and credentials. Never paste tokens into prompts, +files or command examples. A missing connection is a capability gap, not a reason +to bypass authentication with curl or copied credentials. + +## Discover → execute → verify + +1. Inspect the tools actually exposed by the host. Their current descriptions + own API names, parameter schemas and authentication behavior. +2. Use `search_seqera_api` with the operation's intent. Read the returned full + schema, including optional fields, nesting and types; suggestions alone may + omit optional launch settings. Resolve workspace/resource IDs from returned + metadata rather than guessing. +3. Use `call_seqera_api` with the discovered service, exact `api_name` and + schema-shaped parameters. This is not a raw HTTP method/endpoint/body API. +4. For mutations, confirm the authorized scope and verify the resulting state + with an authoritative read. Broaden discovery or report a capability gap when + an operation is unavailable; do not fabricate names or mirror API schemas. + +For resume, discover the existing-workflow resume operation and preserve the +original launch/session relationship. A Platform workflow ID is not a Nextflow +session UUID. For saved-pipeline or ad-hoc launch, follow `launch-workflow`'s +relevant procedure and preserve the selected revision, parameters and lineage. + +Use exposed nf-core discovery helpers for module selection and inspect their +input/output contracts. Workspace execution, resource access and artifact +handoff remain host responsibilities; a tool response is not proof that a +container or pipeline ran successfully. diff --git a/skills/nf-plugin-development/SKILL.md b/packs/nextflow-plugins/skills/nf-plugin-development/SKILL.md similarity index 93% rename from skills/nf-plugin-development/SKILL.md rename to packs/nextflow-plugins/skills/nf-plugin-development/SKILL.md index a3a6553..7103a1e 100644 --- a/skills/nf-plugin-development/SKILL.md +++ b/packs/nextflow-plugins/skills/nf-plugin-development/SKILL.md @@ -6,6 +6,10 @@ description: > executors, trace observers), project structure, testing, and publishing. Use when the user wants to create a new plugin or add custom functionality to Nextflow. --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -15,7 +19,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -493,6 +497,10 @@ void onFlowComplete(WorkflowMetadata meta) { ## Related Skills -- `nf-plugin-legacy-migration` — Convert legacy plugins to new registry format +- [legacy plugin migration](references/nf-plugin-legacy-migration/README.md) — Convert legacy plugins to new registry format - `nextflow-config` — Configure plugins in nextflow.config - `nf-pipeline-design` — Standard pipeline organization + +## Legacy plugin migration + +When migrating an existing legacy plugin, preserve extension behavior and validate the target registry and Nextflow release; publishing needs explicit authorization. Read [legacy plugin migration](references/nf-plugin-legacy-migration/README.md) before proceeding. diff --git a/skills/nf-plugin-legacy-migration/SKILL.md b/packs/nextflow-plugins/skills/nf-plugin-development/references/nf-plugin-legacy-migration/README.md similarity index 90% rename from skills/nf-plugin-legacy-migration/SKILL.md rename to packs/nextflow-plugins/skills/nf-plugin-development/references/nf-plugin-legacy-migration/README.md index 277c3f4..24041ce 100644 --- a/skills/nf-plugin-legacy-migration/SKILL.md +++ b/packs/nextflow-plugins/skills/nf-plugin-development/references/nf-plugin-legacy-migration/README.md @@ -1,11 +1,3 @@ ---- -name: nf-plugin-legacy-migration -description: > - Migrate legacy Nextflow plugins to the new plugin registry format. Covers converting - plugins that use the old GitHub-based nf-plugins-index to the modern registry.nextflow.io - approach. Use when the user has an existing plugin using the legacy format or wants - to understand the differences between old and new plugin systems. ---- ## Using this skill @@ -15,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -127,4 +119,4 @@ If observers are not called, inspect interface compatibility and factory registr - https://github.com/nextflow-io/nf-plugin-template - https://registry.nextflow.io -Use nf-plugin-development for new plugins and nextflow-config for pipeline plugin configuration. +Use `nextflow-plugins:nf-plugin-development` for new plugins and nextflow-config for pipeline plugin configuration. diff --git a/packs/nextflow-plugins/sources.json b/packs/nextflow-plugins/sources.json new file mode 100644 index 0000000..80a09bb --- /dev/null +++ b/packs/nextflow-plugins/sources.json @@ -0,0 +1,211 @@ +{ + "portal_commit": "684d343e75ec6437d58c3e85279a8031384f3b62", + "github_upstreams": [ + { + "repository": "https://github.com/nextflow-io/agent-skills", + "requested_ref": "master", + "resolved_commit": "1edf73763da408c410074568f228a75fc6d42864", + "archive_url": "https://codeload.github.com/nextflow-io/agent-skills/zip/1edf73763da408c410074568f228a75fc6d42864", + "archive_sha256": "470df4cfaedf5d6230e4fc90de517992340dc20f774cb1b1dab130e31f5e0427", + "adapter_version": "1.0.0", + "skills": [ + "create-workflow", + "install-nextflow", + "launch-workflow", + "migrate-nextflow-code", + "run-module" + ], + "license": "Apache-2.0", + "license_file": "licenses/nextflow-agent-skills-Apache-2.0.txt" + } + ], + "portability_cleanup": { + "version": "0.1.6", + "base_version": "0.1.5", + "reviewed_skills": 50, + "reviewed_markdown_files": 139, + "changed_skill_files": [ + "skills/audit-conversion-readiness/SKILL.md", + "skills/audit-conversion-readiness/references/reference-patterns.md", + "skills/audit-conversion-readiness/references/report-template.md", + "skills/audit-conversion-readiness/references/tool-availability.md", + "skills/build-nextflow-pipeline/SKILL.md", + "skills/ce-credentials-setup/SKILL.md", + "skills/ce-credentials-setup/references/aws-batch.md", + "skills/ce-credentials-setup/references/kubernetes.md", + "skills/ce-credentials-setup/references/seqera-compute.md", + "skills/convert-jupyter-notebook/SKILL.md", + "skills/convert-python-script/SKILL.md", + "skills/convert-r-script/SKILL.md", + "skills/convert-r-script/references/nextflow-dsl2.md", + "skills/convert-r-script/references/r-container-images.md", + "skills/create-container/SKILL.md", + "skills/create-workflow/SKILL.md", + "skills/debug-local-run/SKILL.md", + "skills/debug-seqera-failed-run/SKILL.md", + "skills/debug-seqera-failed-run/references/debug-workflow.md", + "skills/debug-seqera-failed-run/references/failure-patterns.md", + "skills/debug-seqera-failed-run/references/fingerprints-and-cascades.md", + "skills/debug-seqera-failed-run/references/fix-confidence.md", + "skills/debug-seqera-failed-run/references/recurring-failures-and-fix-handoff.md", + "skills/debug-seqera-failed-run/references/resume-and-attempt-history.md", + "skills/enumerate-alternative-tools/SKILL.md", + "skills/find-alternative-tools/SKILL.md", + "skills/generate-pipeline-docs/SKILL.md", + "skills/generate-pipeline-memory/SKILL.md", + "skills/genomics-workflow-acceleration/SKILL.md", + "skills/genomics-workflow-acceleration/references/comparison-checklist.md", + "skills/genomics-workflow-acceleration/references/nf-core-parabricks-map.md", + "skills/genomics-workflow-acceleration/references/parabricks-runtime-readiness.md", + "skills/genomics-workflow-acceleration/references/parabricks-tool-map.md", + "skills/genomics-workflow-acceleration/references/step-consolidation.md", + "skills/genomics-workflow-acceleration/references/workflow-frameworks.md", + "skills/genomics-workflow-acceleration/references/workflow-layout.md", + "skills/install-nextflow/SKILL.md", + "skills/launch-workflow/SKILL.md", + "skills/maintain-nf-core-pipeline/SKILL.md", + "skills/maintain-nf-core-pipeline/references/nf-core-conventions.md", + "skills/maintain-nf-core-pipeline/references/template-merges/README.md", + "skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md", + "skills/migrate-from-snakemake/SKILL.md", + "skills/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md", + "skills/migrate-from-snakemake/references/snakemake-nextflow-playbook.md", + "skills/migrate-from-snakemake/references/snakemake-rules-core.md", + "skills/migrate-from-snakemake/references/snakemake-testing-unit-tests.md", + "skills/migrate-from-snakemake/references/snakemake-writing-workflows.md", + "skills/migrate-nextflow-code/SKILL.md", + "skills/migrate-nextflow-code/references/static-typing-params.md", + "skills/migrate-nextflow-code/references/static-typing-processes.md", + "skills/migrate-nextflow-code/references/static-typing-workflows.md", + "skills/migrate-nextflow-code/references/static-typing.md", + "skills/migrate-nextflow-code/references/strict-syntax.md", + "skills/migrate-nextflow-code/references/topic-channels.md", + "skills/migrate-nextflow-code/references/workflow-outputs.md", + "skills/nextflow-26-syntax/SKILL.md", + "skills/nextflow-config/SKILL.md", + "skills/nextflow-config/references/config-guide.md", + "skills/nextflow-config/references/config-options.md", + "skills/nextflow-development/SKILL.md", + "skills/nextflow-development/references/geo-sra-acquisition.md", + "skills/nextflow-development/references/installation.md", + "skills/nextflow-development/references/pipelines/atacseq.md", + "skills/nextflow-development/references/pipelines/rnaseq.md", + "skills/nextflow-development/references/pipelines/sarek.md", + "skills/nextflow-development/references/troubleshooting.md", + "skills/nextflow-history/SKILL.md", + "skills/nextflow-output-patterns/SKILL.md", + "skills/nextflow-schema/SKILL.md", + "skills/nextflow-schema/references/minimal-launchpad-schema.md", + "skills/nextflow-schema/references/sample-sheet-specification.md", + "skills/nextflow-schema/references/schema-specification.md", + "skills/nf-aggregate/SKILL.md", + "skills/nf-data-lineage/SKILL.md", + "skills/nf-debug/SKILL.md", + "skills/nf-docker-scripts/SKILL.md", + "skills/nf-docker-scripts/references/script-strategies-deep-dive.md", + "skills/nf-migrate-25-04/SKILL.md", + "skills/nf-migrate-25-04/references/upstream-25-04.md", + "skills/nf-pipeline-design/SKILL.md", + "skills/nf-pipeline-structure/SKILL.md", + "skills/nf-plugin-development/SKILL.md", + "skills/nf-plugin-legacy-migration/SKILL.md", + "skills/nf-run-history/SKILL.md", + "skills/nf-schema-migration/SKILL.md", + "skills/nf-schema-migration/references/migration-guide.md", + "skills/nf-storedir/SKILL.md", + "skills/nf-test/SKILL.md", + "skills/nf-test/references/assertions.md", + "skills/nf-test/references/nft-utils.md", + "skills/nf-test/references/plugins.md", + "skills/nf-test/references/test-data.md", + "skills/nf-test/references/troubleshooting.md", + "skills/nf-v2-boolean-params/SKILL.md", + "skills/parabricks/SKILL.md", + "skills/parabricks/references/pbrun-applybqsr.md", + "skills/parabricks/references/pbrun-bam2fq.md", + "skills/parabricks/references/pbrun-bammetrics.md", + "skills/parabricks/references/pbrun-bamsort.md", + "skills/parabricks/references/pbrun-bqsr.md", + "skills/parabricks/references/pbrun-collectmultiplemetrics.md", + "skills/parabricks/references/pbrun-dbsnp.md", + "skills/parabricks/references/pbrun-deepsomatic.md", + "skills/parabricks/references/pbrun-deepvariant.md", + "skills/parabricks/references/pbrun-deepvariant_germline.md", + "skills/parabricks/references/pbrun-fq2bam.md", + "skills/parabricks/references/pbrun-fq2bam_meth.md", + "skills/parabricks/references/pbrun-genotypegvcf.md", + "skills/parabricks/references/pbrun-germline.md", + "skills/parabricks/references/pbrun-giraffe.md", + "skills/parabricks/references/pbrun-haplotypecaller.md", + "skills/parabricks/references/pbrun-indexgvcf.md", + "skills/parabricks/references/pbrun-markdup.md", + "skills/parabricks/references/pbrun-minimap2.md", + "skills/parabricks/references/pbrun-mutectcaller.md", + "skills/parabricks/references/pbrun-ont_germline.md", + "skills/parabricks/references/pbrun-pacbio_germline.md", + "skills/parabricks/references/pbrun-pangenome_aware_deepvariant.md", + "skills/parabricks/references/pbrun-pangenome_germline.md", + "skills/parabricks/references/pbrun-postpon.md", + "skills/parabricks/references/pbrun-prepon.md", + "skills/parabricks/references/pbrun-rna_fq2bam.md", + "skills/parabricks/references/pbrun-somatic.md", + "skills/parabricks/references/pbrun-starfusion.md", + "skills/parabricks/references/runtime-environment.md", + "skills/parabricks/references/tool-index.md", + "skills/repair-nf-test/SKILL.md", + "skills/repair-workflow/SKILL.md", + "skills/repair-workflow/references/repair-checklists.md", + "skills/run-module/SKILL.md", + "skills/search-existing-modules/SKILL.md", + "skills/seqera-cli-agent/README.md", + "skills/seqera-cli-agent/SKILL.md", + "skills/seqera-data-links/SKILL.md", + "skills/seqera-mcp/SKILL.md", + "skills/seqera-mcp/references/tool-schemas.md", + "skills/seqerakit/SKILL.md", + "skills/triage-pipeline-parameters/SKILL.md" + ], + "description": "Generic host instructions with no prescribed filesystem paths, directory layouts, storage destinations or path-based setup recipes. Locations come from the user and execution context." + }, + "relicensed": { + "sources": "portal", + "from": "BUSL-1.1", + "to": "Apache-2.0", + "by": "Seqera Labs, S.L.", + "note": "Portal-derived files bundled in this plugin are distributed under Apache-2.0; see LICENSE and NOTICE." + }, + "files": [ + { + "path": "skills/nf-plugin-development/SKILL.md", + "source": "portal/backend/src/skills/nf-plugin-development/SKILL.md", + "source_sha256": "5a328e82652bbe4d0dfc3afdc3877379ce54e1fea7258b6bbf432692a31ee117", + "bundled_sha256": "3d0a304efea9406afcb31531b8ff0b4eb956dbb922717ea90bbe0d909ca5c46e", + "override": true + }, + { + "path": "skills/nf-plugin-development/references/nf-plugin-legacy-migration/README.md", + "source": "portal/backend/src/skills/nf-plugin-legacy-migration/SKILL.md", + "source_sha256": "635d3c3ad2fb29f77cf4bea08cbea5267b636d45aa697d05302a1081d5545c97", + "bundled_sha256": "44fa88b7e8dcfcc086ded7eab4f74a3c24a6fb585017edb531ab1886de0304b7", + "override": true + }, + { + "path": "references/mcp-connection.md", + "source": "tools/curation/mcp-connection.md", + "source_sha256": "568daae3ffaef7092ccd578cd630d5d0a5741fecfd2914a59192102902b1b652", + "bundled_sha256": "568daae3ffaef7092ccd578cd630d5d0a5741fecfd2914a59192102902b1b652", + "override": false + }, + { + "path": "licenses/nextflow-agent-skills-Apache-2.0.txt", + "source": "https://github.com/nextflow-io/agent-skills/blob/1edf73763da408c410074568f228a75fc6d42864/COPYING", + "source_sha256": "5df2a0d87d6c562f0ea11c688ac52532aa28d744cabc7994ff0537f64b3b3320", + "bundled_sha256": "09e8a9bcec8067104652c168685ab0931e7868f9c8284b66f5ae6edae5f1130b", + "override": true + } + ], + "distribution": { + "plugin": "nextflow-plugins", + "requires_core": "nextflow" + } +} diff --git a/packs/nextflow-provenance/.claude-plugin/plugin.json b/packs/nextflow-provenance/.claude-plugin/plugin.json new file mode 100644 index 0000000..8870efc --- /dev/null +++ b/packs/nextflow-provenance/.claude-plugin/plugin.json @@ -0,0 +1,19 @@ +{ + "version": "0.3.0", + "author": { + "name": "Seqera", + "url": "https://seqera.io" + }, + "homepage": "https://github.com/seqeralabs/nextflow-claude-plugin", + "repository": "https://github.com/seqeralabs/nextflow-claude-plugin", + "license": "Apache-2.0", + "keywords": [ + "nextflow", + "seqera", + "nf-core", + "bioinformatics", + "pipelines" + ], + "name": "nextflow-provenance", + "description": "Optional run/cache history analysis and lineage-store exploration. Requires the enabled nextflow core plugin." +} diff --git a/packs/nextflow-provenance/LICENSE b/packs/nextflow-provenance/LICENSE new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-provenance/LICENSE @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-provenance/NOTICE b/packs/nextflow-provenance/NOTICE new file mode 100644 index 0000000..fc0c769 --- /dev/null +++ b/packs/nextflow-provenance/NOTICE @@ -0,0 +1,21 @@ +Nextflow plugin for Claude +Copyright 2024-2026 Seqera Labs, S.L. + +This product is licensed under the Apache License, Version 2.0 (see LICENSE). + +The Apache-2.0 license covers the files in this repository. The hosted Seqera MCP +server it connects to (https://mcp.seqera.io/mcp) is a separate work, governed by +its own license and Seqera's terms of service. + +It includes software and documentation from the following projects, also under +the Apache License, Version 2.0: + +- nextflow-io/agent-skills (https://github.com/nextflow-io/agent-skills) + Skills: create-workflow, install-nextflow, launch-workflow, + migrate-nextflow-code, run-module; scripts/nextflow-*.sh + License: licenses/nextflow-agent-skills-Apache-2.0.txt + +- nextflow-development skill (bio-research skills) + License: skills/nextflow-development/LICENSE.txt + +Per-file origin and hashes are recorded in sources.json. diff --git a/packs/nextflow-provenance/licenses/nextflow-agent-skills-Apache-2.0.txt b/packs/nextflow-provenance/licenses/nextflow-agent-skills-Apache-2.0.txt new file mode 100644 index 0000000..67db858 --- /dev/null +++ b/packs/nextflow-provenance/licenses/nextflow-agent-skills-Apache-2.0.txt @@ -0,0 +1,175 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. diff --git a/packs/nextflow-provenance/references/mcp-connection.md b/packs/nextflow-provenance/references/mcp-connection.md new file mode 100644 index 0000000..3ad3ac2 --- /dev/null +++ b/packs/nextflow-provenance/references/mcp-connection.md @@ -0,0 +1,30 @@ +# Seqera MCP connection and discovery + +Use the plugin's configured Seqera MCP connection (`https://mcp.seqera.io/mcp`). +The host manages OAuth sign-in and credentials. Never paste tokens into prompts, +files or command examples. A missing connection is a capability gap, not a reason +to bypass authentication with curl or copied credentials. + +## Discover → execute → verify + +1. Inspect the tools actually exposed by the host. Their current descriptions + own API names, parameter schemas and authentication behavior. +2. Use `search_seqera_api` with the operation's intent. Read the returned full + schema, including optional fields, nesting and types; suggestions alone may + omit optional launch settings. Resolve workspace/resource IDs from returned + metadata rather than guessing. +3. Use `call_seqera_api` with the discovered service, exact `api_name` and + schema-shaped parameters. This is not a raw HTTP method/endpoint/body API. +4. For mutations, confirm the authorized scope and verify the resulting state + with an authoritative read. Broaden discovery or report a capability gap when + an operation is unavailable; do not fabricate names or mirror API schemas. + +For resume, discover the existing-workflow resume operation and preserve the +original launch/session relationship. A Platform workflow ID is not a Nextflow +session UUID. For saved-pipeline or ad-hoc launch, follow `launch-workflow`'s +relevant procedure and preserve the selected revision, parameters and lineage. + +Use exposed nf-core discovery helpers for module selection and inspect their +input/output contracts. Workspace execution, resource access and artifact +handoff remain host responsibilities; a tool response is not proof that a +container or pipeline ran successfully. diff --git a/skills/nextflow-history/SKILL.md b/packs/nextflow-provenance/skills/nextflow-history/SKILL.md similarity index 88% rename from skills/nextflow-history/SKILL.md rename to packs/nextflow-provenance/skills/nextflow-history/SKILL.md index 1ed2f3c..c8d69ab 100644 --- a/skills/nextflow-history/SKILL.md +++ b/packs/nextflow-provenance/skills/nextflow-history/SKILL.md @@ -7,6 +7,10 @@ description: > Uses run history, task cache metadata, and Nextflow logs supplied by the user. Also use for narrative recaps, recurring failures and pipeline evolution. --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -16,7 +20,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -37,7 +41,7 @@ not assume a working directory or cache location. - Identify safe cleanup candidates after reviewing the user's retention needs. For failure diagnosis, use the `debug-local-run` skill. For Platform history, -use MCP discovery/execution to retrieve workflows; read [MCP connection](../launch-workflow/references/seqera-mcp/README.md) if connection or discovery guidance is needed. +use MCP discovery/execution to retrieve workflows; read [MCP connection](../../references/mcp-connection.md) if connection or discovery guidance is needed. ## Run-history fields @@ -114,7 +118,7 @@ historical failures from current failures and avoid presenting stale logs as the latest run. Related skills: `nextflow-config`, `debug-local-run`, -`debug-seqera-failed-run`, and [MCP connection](../launch-workflow/references/seqera-mcp/README.md). +`debug-seqera-failed-run`, and [MCP connection](../../references/mcp-connection.md). ## Narrative history analysis diff --git a/skills/nextflow-history/references/nf-run-history/README.md b/packs/nextflow-provenance/skills/nextflow-history/references/nf-run-history/README.md similarity index 94% rename from skills/nextflow-history/references/nf-run-history/README.md rename to packs/nextflow-provenance/skills/nextflow-history/references/nf-run-history/README.md index 3c4af66..8fbfb85 100644 --- a/skills/nextflow-history/references/nf-run-history/README.md +++ b/packs/nextflow-provenance/skills/nextflow-history/references/nf-run-history/README.md @@ -7,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. diff --git a/skills/nf-data-lineage/SKILL.md b/packs/nextflow-provenance/skills/nf-data-lineage/SKILL.md similarity index 92% rename from skills/nf-data-lineage/SKILL.md rename to packs/nextflow-provenance/skills/nf-data-lineage/SKILL.md index db50dc6..e594522 100644 --- a/skills/nf-data-lineage/SKILL.md +++ b/packs/nextflow-provenance/skills/nf-data-lineage/SKILL.md @@ -6,6 +6,10 @@ description: > CLI. Requires Nextflow 25.04+ with lineage.enabled=true. Use when the user asks about provenance, data origins, reproducibility, or output traceability. --- + +## Core prerequisite + +Use this optional pack alongside the enabled `nextflow` core plugin. If a needed core skill is unavailable, ask the user to explicitly install/enable core. Local tasks need no Platform authentication. For Platform operations, use core's shared Seqera connection and request authentication if necessary; do not install plugins or start another MCP connection yourself. ## Using this skill @@ -15,7 +19,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../references/mcp-connection.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. diff --git a/packs/nextflow-provenance/sources.json b/packs/nextflow-provenance/sources.json new file mode 100644 index 0000000..1db2924 --- /dev/null +++ b/packs/nextflow-provenance/sources.json @@ -0,0 +1,218 @@ +{ + "portal_commit": "684d343e75ec6437d58c3e85279a8031384f3b62", + "github_upstreams": [ + { + "repository": "https://github.com/nextflow-io/agent-skills", + "requested_ref": "master", + "resolved_commit": "1edf73763da408c410074568f228a75fc6d42864", + "archive_url": "https://codeload.github.com/nextflow-io/agent-skills/zip/1edf73763da408c410074568f228a75fc6d42864", + "archive_sha256": "470df4cfaedf5d6230e4fc90de517992340dc20f774cb1b1dab130e31f5e0427", + "adapter_version": "1.0.0", + "skills": [ + "create-workflow", + "install-nextflow", + "launch-workflow", + "migrate-nextflow-code", + "run-module" + ], + "license": "Apache-2.0", + "license_file": "licenses/nextflow-agent-skills-Apache-2.0.txt" + } + ], + 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Locations come from the user and execution context." + }, + "relicensed": { + "sources": "portal", + "from": "BUSL-1.1", + "to": "Apache-2.0", + "by": "Seqera Labs, S.L.", + "note": "Portal-derived files bundled in this plugin are distributed under Apache-2.0; see LICENSE and NOTICE." + }, + "files": [ + { + "path": "skills/nextflow-history/SKILL.md", + "source": "portal/backend/src/skills/nextflow-history/SKILL.md", + "source_sha256": "4f2ce1b1d39236f1f5b1d7de1ae07d3324b2b8cc32c79e3c6821f43cd2e09bd4", + "bundled_sha256": "8dfdc0a483ef7ea69a1ac0d93f1e88f46bbd619f6c062d32d935f6016c9e94c7", + "override": true + }, + { + "path": "skills/nf-data-lineage/SKILL.md", + "source": "portal/backend/src/skills/nf-data-lineage/SKILL.md", + "source_sha256": "81f88126cf85d2da22f03f7f5ae3c38256b63cccc5350cfc7348e55631ca92a7", + "bundled_sha256": "175450ad1b0f9873b1588b5c2ac5bf87891d8b7ada679a7325c0b2be57053e7d", + "override": true + }, + { + "path": "skills/nextflow-history/references/nf-run-history/README.md", + "source": "portal/backend/src/skills/nf-run-history/SKILL.md", + "source_sha256": "8bcb5e04a79bb28b0cb833e5fdf32f7d81a79eaee81e2e97d2316b486dc3502c", + "bundled_sha256": "4c0985d0a545e61943c644427c345e20459a56d7e8f911d1a1e4010d9bb58cef", + "override": true + }, + { + "path": "references/mcp-connection.md", + "source": "tools/curation/mcp-connection.md", + "source_sha256": "568daae3ffaef7092ccd578cd630d5d0a5741fecfd2914a59192102902b1b652", + "bundled_sha256": "568daae3ffaef7092ccd578cd630d5d0a5741fecfd2914a59192102902b1b652", + "override": false + }, + { + "path": "licenses/nextflow-agent-skills-Apache-2.0.txt", + "source": "https://github.com/nextflow-io/agent-skills/blob/1edf73763da408c410074568f228a75fc6d42864/COPYING", + "source_sha256": "5df2a0d87d6c562f0ea11c688ac52532aa28d744cabc7994ff0537f64b3b3320", + "bundled_sha256": "09e8a9bcec8067104652c168685ab0931e7868f9c8284b66f5ae6edae5f1130b", + "override": true + } + ], + "distribution": { + "plugin": "nextflow-provenance", + "requires_core": "nextflow" + } +} diff --git a/skills/build-nextflow-pipeline/SKILL.md b/skills/build-nextflow-pipeline/SKILL.md index 6eb17b6..31b6d02 100644 --- a/skills/build-nextflow-pipeline/SKILL.md +++ b/skills/build-nextflow-pipeline/SKILL.md @@ -1,17 +1,17 @@ --- name: build-nextflow-pipeline description: > - Plan and scaffold a new Nextflow DSL2 pipeline from source material — - scripts, repositories, Jupyter/R notebooks, papers, or informal - instructions. Drives the planning phases before any .nf code is written: - mapping the data flow, critiquing it, shaping channels and metadata, - scoping subworkflows, hunting for existing modules, and only then building - containers and writing code. Use this skill whenever the user asks to - "build a pipeline", "compose registry modules", "port this to Nextflow", "turn this notebook/repo/script - into a pipeline", or otherwise wants to go from an existing body of work to - a clean Nextflow pipeline. Pair with `nf-pipeline-design`, which owns the - code-level rules (layout, main.nf, subworkflow/module shape); this skill - owns the planning process that precedes them. + Build or convert Nextflow pipelines from scripts, notebooks, repositories + or Snakemake workflows. Also use for read-only conversion readiness audits, + discovering or directly running registry modules, requested tool comparisons, + and Nextflow installation or upgrade help. Choose the bounded task path; + only full pipeline construction uses the planning phases. Pair with + nf-pipeline-design for code structure and output contracts. + Route compute/credential setup to the optional nextflow-platform pack, + nf-core analysis/maintenance to nextflow-nf-core, extension plugin work to + nextflow-plugins, and broad run/cache/lineage analysis to nextflow-provenance. + If a specialist is absent, name its pack from the nextflow-claude-plugin + marketplace and ask the user to explicitly install/enable it; stop that task. --- @@ -30,9 +30,17 @@ manages OAuth for the connected MCP server. # Build a Nextflow Pipeline +## Choose the requested task + +For compute/credential setup, omics analysis/nf-core maintenance, extension plugin development or broad provenance work, read [optional pack handoffs](references/optional-packs.md) first. If the matching namespaced specialist is absent, name its pack, explain explicit installation/enablement and stop that specialist task. These requests do not enter construction phases. + +For an audit-only request, use the conversion-readiness playbook and return its report without writing pipeline code. For module discovery or a single module run, use the matching playbook and stop with a reuse verdict or verified run result. For tool comparison or runtime setup, use only that playbook and stop at the requested answer or authorized environment change. + +These bounded paths skip the full construction phases below. When delegating a helper task, supply the relevant playbook content rather than invoking a removed skill identity. + ## Choose the construction path -For composing existing Registry modules, read [registry composition](references/create-workflow/README.md) and follow its plan → approval → module validation → composition → end-to-end verification loop. For a single module, use `run-module`; a wrapper workflow is unnecessary. +For composing existing Registry modules, read [registry composition](references/create-workflow/README.md) and follow its plan → approval → module validation → composition → end-to-end verification loop. For a single module, use [native module execution](references/run-module/README.md); a wrapper workflow is unnecessary. For scripts, notebooks, repositories or analysis descriptions, use the source-material phases below. Load `nf-pipeline-design` for code-level rules in either path. @@ -50,12 +58,12 @@ Delegate only when the host supports subagents; otherwise perform the same steps | Phase step | Delegate? | Companion skill | |---|---|---| -| Auditing what the source material actually points at | **Yes** — hand the source material to one subagent | `audit-conversion-readiness` | +| Auditing what the source material actually points at | **Yes** — hand the source material to one subagent | [conversion readiness](references/audit-conversion-readiness/README.md) | | Mapping the data flow | No — this is the core act of planning, keep it in the main conversation | — | | Triaging parameters and drafting `nextflow_schema.json` | **Yes** — hand the source material to one subagent | `nextflow-schema` | | Designing channels and metadata | No — needs the data flow map as live context | — | -| Comparing alternatives, only when requested or the selected tool is blocked | **Optional** — delegate the bounded comparison when useful | `find-alternative-tools` | -| Searching for existing Nextflow modules for each chosen tool | **Yes — one subagent per tool, in parallel** | `search-existing-modules` | +| Comparing alternatives, only when requested or the selected tool is blocked | **Optional** — delegate the bounded comparison when useful | [tool comparison](references/find-alternative-tools/README.md) | +| Searching for existing Nextflow modules for each chosen tool | **Yes — one subagent per tool, in parallel** | [module discovery](references/search-existing-modules/README.md) | | Building and verifying the container for each tool branch | **Yes — one subagent per tool, in parallel** | `create-container` | | Writing `main.nf`, subworkflows, and modules | No — this is a synthesis step that uses every prior artifact | — | @@ -100,7 +108,7 @@ available: absolute paths into a lab NAS, reference bundles nobody can reach fro here, a helper script that never made it into the handover. Finding that out after the modules exist is the most expensive way to learn it. -Run `audit-conversion-readiness` on the source material first. It +Run [conversion readiness](references/audit-conversion-readiness/README.md) on the source material first. It returns a blockers-first report — unreachable paths, missing tool code, tools with no distributable container — plus one consolidated list of what to ask the user. Fold the surviving references into Phase 1's data flow map and parameter triage. @@ -346,7 +354,7 @@ Each subworkflow should: Use the tool requested by the user or required to preserve the source analysis. If none is specified, recommend one suitable default and resolve material license, compute or output-contract constraints before implementation. -Use `find-alternative-tools` only when the user requests a comparison or the selected tool is blocked. Research produces candidates; it does not authorize implementing them. +Use [tool comparison](references/find-alternative-tools/README.md) only when the user requests a comparison or the selected tool is blocked. Research produces candidates; it does not authorize implementing them. Add multiple tool branches only when the user explicitly requests or approves them. For approved branches: @@ -365,7 +373,7 @@ For each selected tool, search for existing implementations in this priority ord 2. **The inputted source.** Check the scripts, notebooks, or repository you were given — is there already a containerized version, a Dockerfile, a conda env? Reuse it. 3. **Online: papers, preprints, GitHub, biorxiv, arxiv.** Look for community implementations, reference pipelines, or tool authors' recommended invocations. A five-minute search often finds a canonical invocation that saves hours of trial and error. -**Delegate this search when available.** For each tool selected, use the `search-existing-modules` skill with the tool name, the path to the pipeline's source material, and — if the prior enumerate step flagged one — the nf-core module hint. The hint enables a quick verification instead of re-running the full priority-order search. These tasks can run in parallel with one subagent per tool. Each search produces a verdict (reuse / vendor / write new) plus the structured metadata needed by the next phase. Paste the verdicts into the planning document's "Module sourcing" section. +**Delegate this search when available.** For each tool selected, use the [module discovery](references/search-existing-modules/README.md) skill with the tool name, the path to the pipeline's source material, and — if the prior enumerate step flagged one — the nf-core module hint. The hint enables a quick verification instead of re-running the full priority-order search. These tasks can run in parallel with one subagent per tool. Each search produces a verdict (reuse / vendor / write new) plus the structured metadata needed by the next phase. Paste the verdicts into the planning document's "Module sourcing" section. If a verdict reveals tool-argument parameters that were not captured in Phase 1's schema draft (e.g. the canonical invocation uses a `--kmer-size` flag that the source material omitted), add them to `nextflow_schema.json` now — this is the second expected schema augmentation. Keep `nextflow.config` in sync. @@ -387,7 +395,7 @@ Why this ordering matters: most "Nextflow bugs" when porting existing work are n **Delegate per-tool container builds when available.** For each tool that came back as "vendor" or "write new" from the module search, use the `create-container` skill with: - The tool name and target version. -- The target command line (from the `CANONICAL CLI` field of the search-existing-modules verdict). +- The target command line (from the `CANONICAL CLI` field of the [module discovery](references/search-existing-modules/README.md) verdict). - The test-input row for that tool from the planning document's "Test inputs" section (produced by `nextflow-schema` in Phase 1). Include path, format, size, and expected output shape. - Any constraints the main conversation has committed to (executor, GPU, container registry). @@ -418,7 +426,7 @@ Writing the actual `main.nf`, subworkflows, and modules should now be a mechanic - [ ] Cheap operations are assigned to operators/Groovy; expensive ones to modules - [ ] Each subworkflow has a one-sentence rationale and a named underlying tool (or set of alternative tools with branching) - [ ] The selected tools match the requested analysis; any additional implemented branches were explicitly requested or approved -- [ ] Existing-module search has been done for every chosen tool, using `search-existing-modules`, with verdicts in the planning document +- [ ] Existing-module search has been done for every chosen tool, using [module discovery](references/search-existing-modules/README.md), with verdicts in the planning document - [ ] Test inputs exist at the user's selected test data (or are specified to be derived) for every heavy tool - [ ] Containers are built and tool commands verified, delegated to `create-container` subagents where possible, with verified image references in the planning document - [ ] `nf-pipeline-design` has been re-read for the code-level rules @@ -445,3 +453,34 @@ When converting R source into Nextflow, preserve statistical semantics, dependen ## Notebook conversion playbook When converting a Jupyter notebook, inventory cell dependencies and hidden state before extracting executable steps. Read [notebook conversion](references/convert-jupyter-notebook/README.md) before proceeding. + +## Snakemake conversion playbook + +When converting a Snakefile, preserve DAG, wildcard, scheduler and golden-output semantics. Read [snakemake conversion](references/migrate-from-snakemake/README.md) before proceeding. + +## Conversion readiness playbook + +For an audit-only request, inventory and probe inputs, code and dependencies; stop with a blockers-first report without editing pipeline code. Read [conversion readiness](references/audit-conversion-readiness/README.md) before proceeding. + +## Module discovery playbook + +When selecting a tool implementation, return a verified reuse, vendor/adapt or write-new verdict. Read [module discovery](references/search-existing-modules/README.md) before proceeding. + +## Native module execution playbook + +For a module-only request, inspect the module contract and run it natively on verified inputs; no wrapper workflow or construction phases are needed. Read [native module execution](references/run-module/README.md) before proceeding. + +## Tool comparison playbook + +For requested comparisons or a blocked selected tool, compare alternatives; implementation needs separate user approval. Read [tool comparison](references/find-alternative-tools/README.md) before proceeding. + +## Runtime setup playbook + +For installation or upgrade help, check the selected release and operation first; ask before changing the environment. Read [runtime setup](references/install-nextflow/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. + +When editing an nf-core project, read [nf-core safety](references/nf-core-safety.md); basic safe edits do not require the optional maintenance pack. diff --git a/skills/audit-conversion-readiness/SKILL.md b/skills/build-nextflow-pipeline/references/audit-conversion-readiness/README.md similarity index 77% rename from skills/audit-conversion-readiness/SKILL.md rename to skills/build-nextflow-pipeline/references/audit-conversion-readiness/README.md index a4cec13..eeebf3e 100644 --- a/skills/audit-conversion-readiness/SKILL.md +++ b/skills/build-nextflow-pipeline/references/audit-conversion-readiness/README.md @@ -1,18 +1,3 @@ ---- -name: audit-conversion-readiness -description: > - Read-only first-pass audit of source material (scripts, notebooks, - Snakemake/WDL/CWL workflows, legacy in-house pipelines) before converting or - migrating it to Nextflow. Inventories every hardcoded or external file path, - probes which of them are actually reachable from this session, and flags tool - code and dependencies that are referenced but were never provided. Run this - before any conversion work, and whenever the user asks to "audit this before - converting", "find the hardcoded paths", "can you actually access these files - or reference data", "what's missing before we convert this", "what will block - this port to Nextflow", or "why can't you read this path". Output is a - blockers-first report plus one consolidated list of what the user needs to - supply — no pipeline code. ---- ## Using this skill @@ -22,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -106,7 +91,7 @@ names — you must then `call_seqera_api` to list them (the authenticated MCP co returned by an authenticated workspace lookup 3. Match each `s3://` / `gs://` / `az://` URI against the returned links -Load `seqera-data-links` only if you then need to *create* a link. +Load `nextflow-platform:seqera-data-links` only if you then need to *create* a link. An existing data link is usually the answer to "how will the pipeline read this". ## Step 3 — audit tool and helper code availability @@ -145,16 +130,16 @@ exists to prevent. With the audit answered, route onward: -- [parameter triage](../nextflow-schema/references/triage-pipeline-parameters/README.md) — turn the surviving paths and +- [parameter triage](../../../nextflow-schema/references/triage-pipeline-parameters/README.md) — turn the surviving paths and constants into a parameter surface and schema -- `create-container` or `nf-docker-scripts` — tools +- `create-container` or [script packaging](../../../create-container/references/nf-docker-scripts/README.md) — tools with no usable image -- `search-existing-modules` — tools that may already have a module -- `find-alternative-tools` — tools blocked by license, GPU +- [module discovery](../search-existing-modules/README.md) — tools that may already have a module +- [tool comparison](../find-alternative-tools/README.md) — tools blocked by license, GPU requirements, or abandonment -- `seqera-data-links` — cloud data the pipeline must read -- Then the conversion skill itself: [Python conversion](../build-nextflow-pipeline/references/convert-python-script/README.md), [R conversion](../build-nextflow-pipeline/references/convert-r-script/README.md), - [notebook conversion](../build-nextflow-pipeline/references/convert-jupyter-notebook/README.md), `migrate-from-snakemake`, or [registry composition](../build-nextflow-pipeline/references/create-workflow/README.md) +- `nextflow-platform:seqera-data-links` — cloud data the pipeline must read +- Then the conversion skill itself: [Python conversion](../convert-python-script/README.md), [R conversion](../convert-r-script/README.md), + [notebook conversion](../convert-jupyter-notebook/README.md), [snakemake conversion](../migrate-from-snakemake/README.md), or [registry composition](../create-workflow/README.md) ## Guardrails @@ -165,5 +150,5 @@ With the audit answered, route onward: - Never treat a missing file as a reason to drop the step from the conversion — it is a question for the user. - Hardcoded paths are findings, not bugs to fix in place. The pipeline's - parameter surface is where they get resolved, in [parameter triage](../nextflow-schema/references/triage-pipeline-parameters/README.md). + parameter surface is where they get resolved, in [parameter triage](../../../nextflow-schema/references/triage-pipeline-parameters/README.md). - Keep the audit read-only. No edits to the source material, no scaffolding. diff --git a/skills/audit-conversion-readiness/references/reference-patterns.md b/skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/reference-patterns.md similarity index 100% rename from skills/audit-conversion-readiness/references/reference-patterns.md rename to skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/reference-patterns.md diff --git a/skills/audit-conversion-readiness/references/report-template.md b/skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/report-template.md similarity index 100% rename from skills/audit-conversion-readiness/references/report-template.md rename to skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/report-template.md diff --git a/skills/audit-conversion-readiness/references/tool-availability.md b/skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/tool-availability.md similarity index 98% rename from skills/audit-conversion-readiness/references/tool-availability.md rename to skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/tool-availability.md index d3788e4..5179582 100644 --- a/skills/audit-conversion-readiness/references/tool-availability.md +++ b/skills/build-nextflow-pipeline/references/audit-conversion-readiness/references/tool-availability.md @@ -67,7 +67,7 @@ just the Dockerfile: cannot fetch these unattended; they become a staged input or a data link. - **GPU-only** — a GPU requirement constrains the compute environment. Record the CUDA/driver expectation. If the target environment has no GPU, route to - `find-alternative-tools` for a CPU path. + [tool comparison](../../find-alternative-tools/README.md) for a CPU path. - **Interactive or GUI-only** — cannot be a pipeline step at all. It needs either a headless mode or removal from scope. - **Abandoned with no image and no source release** — treat like a missing tool diff --git a/skills/build-nextflow-pipeline/references/convert-jupyter-notebook/README.md b/skills/build-nextflow-pipeline/references/convert-jupyter-notebook/README.md index 5bce8de..adb6dbd 100644 --- a/skills/build-nextflow-pipeline/references/convert-jupyter-notebook/README.md +++ b/skills/build-nextflow-pipeline/references/convert-jupyter-notebook/README.md @@ -28,7 +28,7 @@ Identify meaningful executable tasks rather than making each cell a process. Ext ### Plan First 0. **Audit** what the notebook points at — run - `audit-conversion-readiness` to find hardcoded paths you cannot + [conversion readiness](../audit-conversion-readiness/README.md) to find hardcoded paths you cannot reach and helper modules the notebook imports but that were not provided 1. **Analyze** the notebook: understand the analysis steps, inputs, outputs, and dependencies between cells 2. **Outline** the Nextflow process structure: identify logical groupings of cells that form distinct pipeline steps @@ -54,7 +54,7 @@ After generating the pipeline: Run validation with an available Nextflow installation and host execution tools. If either is unavailable, report validation as unverified and read -`install-nextflow` for installation guidance. +[runtime setup](../install-nextflow/README.md) for installation guidance. ### Common Patterns diff --git a/skills/build-nextflow-pipeline/references/convert-python-script/README.md b/skills/build-nextflow-pipeline/references/convert-python-script/README.md index 0efefe6..b5497b5 100644 --- a/skills/build-nextflow-pipeline/references/convert-python-script/README.md +++ b/skills/build-nextflow-pipeline/references/convert-python-script/README.md @@ -27,7 +27,7 @@ Load this skill when the user wants to: ## Workflow -0. **Audit readiness** — `audit-conversion-readiness` for anything +0. **Audit readiness** — [conversion readiness](../audit-conversion-readiness/README.md) for anything beyond a self-contained script: it finds hardcoded paths you cannot reach and imports or helper scripts that were never provided, before you design around them. @@ -228,7 +228,7 @@ Map Python's `shutil.copy(result, output_dir)` or `os.rename()` calls → `publi ## Snakemake Migration -For full Snakemake workflow conversion, load the dedicated `migrate-from-snakemake` skill. +For full Snakemake workflow conversion, load the dedicated [snakemake conversion](../migrate-from-snakemake/README.md) skill. This skill focuses on standalone Python script conversion. ## Common Pitfalls diff --git a/skills/build-nextflow-pipeline/references/convert-r-script/README.md b/skills/build-nextflow-pipeline/references/convert-r-script/README.md index 005c38c..d7b821d 100644 --- a/skills/build-nextflow-pipeline/references/convert-r-script/README.md +++ b/skills/build-nextflow-pipeline/references/convert-r-script/README.md @@ -22,7 +22,7 @@ Convert R source while preserving statistical behavior. Wrap tested R code when ### 0. Audit readiness For anything beyond a self-contained script, run -`audit-conversion-readiness` first. `setwd()` plus relative reads, +[conversion readiness](../audit-conversion-readiness/README.md) first. `setwd()` plus relative reads, `source()` of files outside the handover, and reference paths on a lab share are the usual blockers, and they are cheaper to surface now than mid-conversion. @@ -60,7 +60,7 @@ After generating the pipeline: Run validation with an available Nextflow installation and host execution tools. If either is unavailable, report validation as unverified and read -`install-nextflow` for installation guidance. +[runtime setup](../install-nextflow/README.md) for installation guidance. ## Guidelines diff --git a/skills/build-nextflow-pipeline/references/create-workflow/README.md b/skills/build-nextflow-pipeline/references/create-workflow/README.md index 2280718..49a24fb 100644 --- a/skills/build-nextflow-pipeline/references/create-workflow/README.md +++ b/skills/build-nextflow-pipeline/references/create-workflow/README.md @@ -30,12 +30,12 @@ include { FASTQC } from 'nf-core/fastqc' workflow { FASTQC(Channel.fromPath(params.input)) } ``` -✅ **CORRECT** - Use the `run-module` skill: +✅ **CORRECT** - Use the [native module execution](../run-module/README.md) skill: ``` -run-module +[native module execution](../run-module/README.md) ``` -**The `run-module` skill:** +**The [native module execution](../run-module/README.md) skill:** - Uses `nextflow module search/view` to discover and get proper inputs/parameters - Runs modules directly via `nextflow module run /` - No wrapper workflow needed @@ -74,13 +74,13 @@ run-module 1. Determine appropriate **test data** for validation 2. For EACH module in the plan, sequentially: - - **Install and run with test data**: Invoke `run-module` + - **Install and run with test data**: Invoke [native module execution](../run-module/README.md) - **Verify outputs** - confirm expected data is produced - Only proceed to next module after current one succeeds 3. Record ALL module run commands and their outputs in a validation record selected by the user 4. If a command fails, stop and show the user the command used and the output generated before trying something else -> **Note**: The `run-module` skill uses `nextflow module` commands for discovery, configuration, and execution — modules are installed on-the-fly. +> **Note**: The [native module execution](../run-module/README.md) skill uses `nextflow module` commands for discovery, configuration, and execution — modules are installed on-the-fly. **DO NOT proceed to Step 4 until ALL modules have been individually validated.** @@ -125,7 +125,7 @@ Only after ALL modules run successfully: ### Module Selection - Prefer single-tool modules over sub-workflows -- Do not write wrapper workflows to test single modules - use `run-module` instead +- Do not write wrapper workflows to test single modules - use [native module execution](../run-module/README.md) instead - Use `nextflow module search` to find modules, then `nextflow module view` for details ### Debugging Protocol @@ -140,17 +140,17 @@ Only after ALL modules run successfully: | Task | Invoke Skill | |------|--------------| -| Install/run/test a module | `run-module` | +| Install/run/test a module | [native module execution](../run-module/README.md) | ### When to Delegate -- **Step 3 (Validate Modules)**: Use `run-module` skill for each module validation +- **Step 3 (Validate Modules)**: Use [native module execution](../run-module/README.md) skill for each module validation ### Example: Step 3 Validation For each module in your plan: ``` -1. Invoke: run-module → install, run with test data, and verify outputs +1. Invoke: [native module execution](../run-module/README.md) → install, run with test data, and verify outputs 2. Only proceed to next module after success ``` diff --git a/skills/find-alternative-tools/SKILL.md b/skills/build-nextflow-pipeline/references/find-alternative-tools/README.md similarity index 79% rename from skills/find-alternative-tools/SKILL.md rename to skills/build-nextflow-pipeline/references/find-alternative-tools/README.md index d1d5324..17ad06a 100644 --- a/skills/find-alternative-tools/SKILL.md +++ b/skills/build-nextflow-pipeline/references/find-alternative-tools/README.md @@ -1,7 +1,3 @@ ---- -name: find-alternative-tools -description: Given a named bioinformatics analysis step (e.g. "multiple sequence alignment", "somatic variant calling", "protein structure prediction", "single-cell demultiplexing"), find the credible alternative tools that could implement it, with pros/cons, license notes, typical compute requirements, maintenance status, and a ranked recommendation. Output is a structured comparison to inform tool selection; research does not authorize implementation of additional branches. Use whenever a subworkflow is being scoped and needs multiple tool options, when asked to "list alternatives for X", "what could we use instead of Y", "what tools exist for Z", or as a subagent task inside the `build-nextflow-pipeline` flow at the alternative-tools step. Self-contained — needs only the analysis step and any constraints, no prior conversation context. ---- ## Using this skill @@ -11,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -52,7 +48,7 @@ For each tool, a short block: - **Maintenance status** — last release date, commit activity, responsive issue tracker - **Compute profile** — CPU-only / GPU-required / memory footprint / typical runtime per sample - **Container availability** — official Docker image, bioconda package, or needs-build-from-source -- **nf-core module hint** — if you happen to notice an existing nf-core module for this tool during your research on a public module page or in the user's source, record it here. This is not the job of this skill (that is `search-existing-modules`), but free signal is free signal — the next phase can verify and skip redundant discovery. +- **nf-core module hint** — if you happen to notice an existing nf-core module for this tool during your research on a public module page or in the user's source, record it here. This is not the job of this skill (that is [module discovery](../search-existing-modules/README.md)), but free signal is free signal — the next phase can verify and skip redundant discovery. - **Output format** — what downstream tools need to consume - **Strengths** — 1–3 bullets, concrete not marketing - **Weaknesses / caveats** — 1–3 bullets, honest; include known bugs, quality issues, or sharp edges diff --git a/skills/install-nextflow/SKILL.md b/skills/build-nextflow-pipeline/references/install-nextflow/README.md similarity index 87% rename from skills/install-nextflow/SKILL.md rename to skills/build-nextflow-pipeline/references/install-nextflow/README.md index 3d38792..2928647 100644 --- a/skills/install-nextflow/SKILL.md +++ b/skills/build-nextflow-pipeline/references/install-nextflow/README.md @@ -1,7 +1,3 @@ ---- -name: install-nextflow -description: Install or upgrade Nextflow on the user's machine. Use when the user wants to install Nextflow, check their current Nextflow version, upgrade Nextflow, or set up the prerequisites (Java 17+) needed to run Nextflow. ---- ## Using this skill @@ -11,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -19,6 +15,8 @@ manages OAuth for the connected MCP server. # Install or Upgrade Nextflow +An installation-help request is not permission to change the environment. Confirm the target release, Java/runtime prerequisites and user's approval before any installer, package-manager command or self-update. + Install Nextflow (or upgrade an existing installation) and ensure the Java prerequisite is in place. ## Step 1: Check Whether Nextflow Is Installed @@ -35,8 +33,8 @@ command -v nextflow && nextflow -version If Nextflow is already installed: 1. Read the installed version from `nextflow -version`. -2. If the installed version is **older than 26.04**, the user MUST upgrade — other Nextflow skills depend on it. -3. Otherwise, propose an upgrade only if a newer version is available. +2. Check whether the installed release supports the user's requested operation. Ordinary pipeline execution does not inherit the 26.04 minimum used by native module or launch commands. +3. If the operation is unsupported, explain the minimum supported release and ask before upgrading; otherwise keep the existing installation unless the user requests an upgrade. Run a self-update (it checks the latest release and updates if newer): diff --git a/skills/migrate-from-snakemake/SKILL.md b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/README.md similarity index 89% rename from skills/migrate-from-snakemake/SKILL.md rename to skills/build-nextflow-pipeline/references/migrate-from-snakemake/README.md index 1e5db01..03cdef7 100644 --- a/skills/migrate-from-snakemake/SKILL.md +++ b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/README.md @@ -1,10 +1,3 @@ ---- -name: migrate-from-snakemake -description: > - Convert Snakemake workflows to idiomatic Nextflow DSL2 pipelines with a - test-first, modular migration loop. Trigger: "snakemake to nextflow", - "migrate from snakemake", "convert snakefile", "/migrate-from-snakemake". ---- ## Using this skill @@ -14,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -49,11 +42,11 @@ Bootstrap these files before any process exists: Check the relevant lint rules, including `nfcore_yml`, `nextflow_config`, `base_config`, `modules_config`, `local_component_structure`, `pipeline_todos`, `template_strings`, and `merge_markers`. Run `nf-core pipelines lint -k --json ` from the pipeline root before declaring the migration done. -For the complete conventions (branches, edit policy, CLI commands), chain `maintain-nf-core-pipeline` and read its `nf-core-conventions.md`. +For nf-core-safe editing, read [nf-core safety](../nf-core-safety.md). Template synchronization or upstream contribution is a separate optional maintenance task. ### 1) Establish source-of-truth before edits -0. **Audit readiness first** — run `audit-conversion-readiness` over +0. **Audit readiness first** — run [conversion readiness](../audit-conversion-readiness/README.md) over the Snakefile and its config. Every `config[...]` key with no configfile entry, every `script:`/`wrapper:` that is not in the handover, and every reference path on an unreachable mount is a blocker that stops a baseline run before it starts. @@ -78,7 +71,7 @@ Treat this as your spec. The rulegraph is your conversion roadmap — each node - Translate the main `Snakefile` into `main.nf` + `nextflow.config` skeleton. - Map global config and top-level DAG flow before implementing every rule detail. - Keep process stubs minimal but executable so the workflow compiles early. -- For non-trivial param surfaces: [parameter triage](../nextflow-schema/references/triage-pipeline-parameters/README.md) before locking `nextflow.config`. +- For non-trivial param surfaces: [parameter triage](../../../nextflow-schema/references/triage-pipeline-parameters/README.md) before locking `nextflow.config`. ### 4) Decompose by responsibility @@ -88,7 +81,7 @@ Treat this as your spec. The rulegraph is your conversion roadmap — each node ### 5) Prefer nf-core modules as starting points -For each wrapper/rule tool, call `search-existing-modules` first — it returns a verdict (reuse nf-core, vendor a community module, or canonical invocation for a project-owned module). Patch only the delta for local behavior. +For each wrapper/rule tool, call [module discovery](../search-existing-modules/README.md) first — it returns a verdict (reuse nf-core, vendor a community module, or canonical invocation for a project-owned module). Patch only the delta for local behavior. ### 6) Wire dataflow explicitly diff --git a/skills/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md similarity index 100% rename from skills/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md rename to skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md diff --git a/skills/migrate-from-snakemake/references/snakemake-nextflow-playbook.md b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-nextflow-playbook.md similarity index 100% rename from skills/migrate-from-snakemake/references/snakemake-nextflow-playbook.md rename to skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-nextflow-playbook.md diff --git a/skills/migrate-from-snakemake/references/snakemake-rules-core.md b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-rules-core.md similarity index 100% rename from skills/migrate-from-snakemake/references/snakemake-rules-core.md rename to skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-rules-core.md diff --git a/skills/migrate-from-snakemake/references/snakemake-testing-unit-tests.md b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-testing-unit-tests.md similarity index 100% rename from skills/migrate-from-snakemake/references/snakemake-testing-unit-tests.md rename to skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-testing-unit-tests.md diff --git a/skills/migrate-from-snakemake/references/snakemake-writing-workflows.md b/skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-writing-workflows.md similarity index 100% rename from skills/migrate-from-snakemake/references/snakemake-writing-workflows.md rename to skills/build-nextflow-pipeline/references/migrate-from-snakemake/references/snakemake-writing-workflows.md diff --git a/skills/build-nextflow-pipeline/references/nf-core-safety.md b/skills/build-nextflow-pipeline/references/nf-core-safety.md new file mode 100644 index 0000000..58a7274 --- /dev/null +++ b/skills/build-nextflow-pipeline/references/nf-core-safety.md @@ -0,0 +1,9 @@ +# nf-core safety in the core plugin + +When a project declares nf-core conventions, preserve its scaffolding, schema, samplesheet checks, software-version emissions and resource profiles. Match publication syntax to the project's supported Nextflow release and existing output contract; legacy examples do not mandate replacing workflow outputs with publishDir. + +Inspect the repository's contribution rules and actual branches before editing. nf-core commonly develops on dev and releases from main/master; verify this repository rather than unconditionally switching branches. Opening or merging PRs requires the user's authorization. + +Shared modules are upstream-owned: avoid silently modifying them in place. Prefer a documented local adapter or approved upstream change; preserve the shared module's input/output contract and dependency pins. Run the applicable installed nf-core lint checks and representative tests before claiming compliance. + +Template synchronization, bulk module updates and upstream contributions are separate maintenance work. If explicitly requested, use `nextflow-nf-core:maintain-nf-core-pipeline` when that pack is enabled. Otherwise explain the missing pack and ask the user to install/enable it; do not silently install plugins or expand a conversion into maintenance. diff --git a/skills/build-nextflow-pipeline/references/optional-packs.md b/skills/build-nextflow-pipeline/references/optional-packs.md new file mode 100644 index 0000000..49b4af7 --- /dev/null +++ b/skills/build-nextflow-pipeline/references/optional-packs.md @@ -0,0 +1,16 @@ +# Optional Nextflow packs + +Inspect the session's available skill inventory before invoking a specialist. If the namespaced skill is available, use it for the requested task. If not, explain which pack is needed and ask the user to explicitly install/enable it. Do not silently install plugins, invoke a missing skill or access paths outside the current plugin root. + +| Requested task | Optional skill | +| --- | --- | +| Create compute environments or credentials | `nextflow-platform:ce-credentials-setup` | +| Create/update storage data links | `nextflow-platform:seqera-data-links` | +| Write declarative Platform provisioning YAML | `nextflow-platform:seqerakit` | +| Run omics analysis or acquire GEO/SRA datasets | `nextflow-nf-core:nextflow-development` | +| Template sync or upstream nf-core maintenance | `nextflow-nf-core:maintain-nf-core-pipeline` | +| Develop or migrate a Nextflow extension plugin | `nextflow-plugins:nf-plugin-development` | +| Broad run/cache history or storage analysis | `nextflow-provenance:nextflow-history` | +| Trace lineage-store output origins | `nextflow-provenance:nf-data-lineage` | + +All packs share the enabled `nextflow` core plugin's hosted Seqera connection. They carry only discovery/safety guidance, not duplicate MCP servers or API schemas. Credential, infrastructure, publication and destructive changes need explicit authorization. Core debugging, run identification, ordinary launch/resume and basic nf-core-safe edits remain available without optional packs. diff --git a/skills/run-module/SKILL.md b/skills/build-nextflow-pipeline/references/run-module/README.md similarity index 91% rename from skills/run-module/SKILL.md rename to skills/build-nextflow-pipeline/references/run-module/README.md index aad186f..d76ebc2 100644 --- a/skills/run-module/SKILL.md +++ b/skills/build-nextflow-pipeline/references/run-module/README.md @@ -1,7 +1,3 @@ ---- -name: run-module -description: Run Nextflow Registry modules natively using `nextflow module` commands. Use when running, listing, or getting info about Nextflow modules. ---- ## Using this skill @@ -11,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. diff --git a/skills/search-existing-modules/SKILL.md b/skills/build-nextflow-pipeline/references/search-existing-modules/README.md similarity index 77% rename from skills/search-existing-modules/SKILL.md rename to skills/build-nextflow-pipeline/references/search-existing-modules/README.md index e258a33..efea2a2 100644 --- a/skills/search-existing-modules/SKILL.md +++ b/skills/build-nextflow-pipeline/references/search-existing-modules/README.md @@ -1,19 +1,3 @@ ---- -name: search-existing-modules -description: > - Given a bioinformatics tool name (e.g. MAFFT, Boltz, bcftools, salmon), - search for existing Nextflow module implementations in priority order — - nf-core/modules first, then a supplied source repository, then the - broader community (GitHub, nf-core pipelines, biorxiv/arxiv - supplementary pipelines). Return a verdict — reuse the nf-core module - at path X, vendor/adapt the module from repo Y, or no existing - implementation (in which case provide the canonical invocation for a - new module). Use whenever a subworkflow is being scoped and needs to - decide whether to reuse an existing Nextflow module or write a new one, - or as a subagent task during the `nf-pipeline-design` / - build-nextflow-pipeline flow. Self-contained — needs only the tool name and - optionally the source repo path, no prior conversation context. ---- ## Using this skill @@ -23,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. diff --git a/skills/create-container/SKILL.md b/skills/create-container/SKILL.md index a6c5ade..7d5b049 100644 --- a/skills/create-container/SKILL.md +++ b/skills/create-container/SKILL.md @@ -1,19 +1,11 @@ --- name: create-container description: > - Build, claim, or recommend a verified container for a bioinformatics tool — - and prove it runs the intended command on representative test data before - handing it off for module authoring. Make sure to use this skill whenever - the user wants to containerize a tool, wrap a tool for a Nextflow module, - set up Wave for a custom package stack, pin a Bioconda/conda-forge - environment, or unblock a "this tool's dependencies are weird" problem. - Trigger phrases include "containerize X", "I need an image for Y", - "set up Wave for Z", "build a conda env for this tool", "verify this - container works on test input", "what container does need", - "wrap for a Nextflow module", "fix this conda solve". Follows a - build → run-test-input → iterate loop and returns a structured handoff - (verified image reference + working command). Do not author the Nextflow - module here — that belongs in `build-nextflow-pipeline` after verification. + Create and verify containers for Nextflow tools using Wave or the selected + runtime. Also use for choosing where process scripts live, helper-command + staging, templates and image packaging. Script-placement advice does not + require building an image. Verify the requested command and representative + outputs before claiming a container works. --- @@ -165,3 +157,12 @@ FAILED ATTEMPTS: 4. When multiple tools belong together, combine them into one container only if they are actually used together 5. If the environment lacks live Wave APIs, still provide the concrete package spec and Nextflow config 6. Do not call a container verified until the command has run on test data or you clearly label it as unverified + +## Script packaging playbook + +For script-placement questions, choose and verify staging or packaging without requiring a container build. Read [script packaging](references/nf-docker-scripts/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. diff --git a/skills/nf-docker-scripts/SKILL.md b/skills/create-container/references/nf-docker-scripts/README.md similarity index 93% rename from skills/nf-docker-scripts/SKILL.md rename to skills/create-container/references/nf-docker-scripts/README.md index 14cc414..fb2f8a0 100644 --- a/skills/nf-docker-scripts/SKILL.md +++ b/skills/create-container/references/nf-docker-scripts/README.md @@ -1,12 +1,3 @@ ---- -name: nf-docker-scripts -description: > - Guide users on how to manage scripts in Nextflow processes and Docker images. - Covers shared helper commands, template directive, inline scripts, and why module - binaries should not be recommended by default. Use when the user asks about - Docker images for Nextflow, where to put scripts, how to handle custom code - in processes, or builds a container that bakes scripts in. ---- ## Using this skill @@ -16,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. @@ -311,6 +302,6 @@ When the user asks about Docker + scripts, follow this flow: ## Related Skills - `create-container` — Wave/conda container provisioning -- [registry composition](../build-nextflow-pipeline/references/create-workflow/README.md) — composing workflows from modules -- [Python conversion](../build-nextflow-pipeline/references/convert-python-script/README.md) — converting Python scripts to Nextflow processes +- [registry composition](../../../build-nextflow-pipeline/references/create-workflow/README.md) — composing workflows from modules +- [Python conversion](../../../build-nextflow-pipeline/references/convert-python-script/README.md) — converting Python scripts to Nextflow processes - `nf-pipeline-design` — understanding pipeline layout including shared helper commands diff --git a/skills/nf-docker-scripts/references/script-strategies-deep-dive.md b/skills/create-container/references/nf-docker-scripts/references/script-strategies-deep-dive.md similarity index 100% rename from skills/nf-docker-scripts/references/script-strategies-deep-dive.md rename to skills/create-container/references/nf-docker-scripts/references/script-strategies-deep-dive.md diff --git a/skills/debug-local-run/SKILL.md b/skills/debug-local-run/SKILL.md index 4adfa16..ab87521 100644 --- a/skills/debug-local-run/SKILL.md +++ b/skills/debug-local-run/SKILL.md @@ -102,3 +102,10 @@ actually run and which remain unverified. References: [Nextflow error handling](https://www.nextflow.io/docs/latest/process.html#error-strategy) and [Nextflow tracing](https://www.nextflow.io/docs/latest/tracing.html). + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. + +For selecting a run or inspecting resume/cache identity, read [run identification](references/run-identification.md); the provenance pack is unnecessary for ordinary diagnosis. diff --git a/skills/debug-local-run/references/run-identification.md b/skills/debug-local-run/references/run-identification.md new file mode 100644 index 0000000..c7d2328 --- /dev/null +++ b/skills/debug-local-run/references/run-identification.md @@ -0,0 +1,9 @@ +# Identify the selected local run before debugging or resuming + +Read history in the environment that owns the run, using the installed release's command help and user-selected workspace. `nextflow log` lists runs; `nextflow log ` retrieves selected task metadata. Record the run name/session ID, pipeline revision, command/parameters, status and work directory before choosing a resume target. + +Confirm that the selected work directory and cache metadata are accessible. A newer run, matching filename or cache hit does not prove that it is the intended analysis. Inspect the selected task's .command files and outputs when diagnosing failures; distinguish cached reuse, submission and completed output verification. + +Read-only inspection does not authorize cleanup, deletion, installation or rerunning a pipeline. Ask for approval before mutations; `nextflow clean` can destroy work required for resume. + +Broad historical recaps and storage analysis belong to `nextflow-provenance:nextflow-history`; output-origin/LID exploration belongs to `nextflow-provenance:nf-data-lineage`. Use those skills only when the optional pack is enabled; ordinary debugging and resume selection do not require it. diff --git a/skills/debug-seqera-failed-run/SKILL.md b/skills/debug-seqera-failed-run/SKILL.md index d1e992a..7884375 100644 --- a/skills/debug-seqera-failed-run/SKILL.md +++ b/skills/debug-seqera-failed-run/SKILL.md @@ -98,3 +98,8 @@ Load this skill when the user wants to: - [Nextflow Platform troubleshooting](https://docs.seqera.io/platform/latest/troubleshooting) - [Nextflow process error strategies](https://www.nextflow.io/docs/latest/process.html#error-strategy) + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. diff --git a/skills/launch-workflow/SKILL.md b/skills/launch-workflow/SKILL.md index 8f801c0..aa4a8b2 100644 --- a/skills/launch-workflow/SKILL.md +++ b/skills/launch-workflow/SKILL.md @@ -1,6 +1,11 @@ --- name: launch-workflow -description: Launch Nextflow pipeline executions on cloud and HPC clusters via Nextflow Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Nextflow Platform. +description: > + Plan, launch or resume Nextflow pipelines locally or through Nextflow Platform. + Use for pre-launch questions about uncommitted/unpublished changes, revision + selection, parameters, compute resources and resume identity, as well as + submission and readback. Publication and infrastructure creation require + separate explicit authorization; a launch question does not authorize them. --- @@ -17,7 +22,17 @@ describe API operations. Discover their exact names and parameter schemas with manages OAuth for the connected MCP server. -# Launch Pipeline on Nextflow Platform +# Launch or Resume a Pipeline + +## Local runs and resume + +For a local run, confirm the user's pipeline, parameters, executor and output destination. Use the installed release's `nextflow run` interface; a local run does not require Platform authentication, a remote Git repository or Nextflow 26.04. + +Before resuming, read [run identification](../debug-local-run/references/run-identification.md) and verify the requested run/session and accessible work/cache metadata. Use `-resume` with the selected identity; do not choose a run solely because it is newest. Inspect completion status and representative outputs; a cache hit alone is not scientific-output verification. + +For missing runtime setup, read [runtime setup](../build-nextflow-pipeline/references/install-nextflow/README.md). Stop before installing or upgrading without explicit approval. + +## Platform launches Launch Nextflow pipeline executions on cloud (AWS, Google Cloud, Azure) and HPC clusters (Slurm, LSF, etc.) through Nextflow Platform. Nextflow Platform manages the target compute environment, executes the pipeline from a remote Git repository, and provides monitoring. @@ -27,7 +42,7 @@ Launch Nextflow pipeline executions on cloud (AWS, Google Cloud, Azure) and HPC 1. **Configure the compute environment** — select a Nextflow Platform compute environment for the target cloud or cluster. 2. **Ensure the pipeline is in a remote Git repository** — Nextflow Platform launches pipelines from GitHub (or a compatible Git host such as GitLab or Bitbucket). If the local pipeline is not yet hosted, assist the user in setting up the repository. -3. **Upload local changes** — push any uncommitted local changes to the remote so the launched run reflects the user's current code. +3. **Select a published revision** — verify that the remote contains the intended code. Publishing local changes requires separate explicit approval; a launch request alone is not authority to commit or push. 4. **Launch with `nextflow launch`** — submit the pipeline by passing the Git repository URL and the expected parameters. ## Step 1: Authenticate with Nextflow Platform @@ -78,16 +93,11 @@ git status **If the pipeline is not yet a Git repository or has no remote**, assist the user in setting it up: -Initialize Git if needed, review the user's selected pipeline files, and stage -only the intended changes. Help the user create or select a remote repository, -configure its remote URL, and push the agreed revision using the available tools. +Explain the missing published revision and ask for separate authorization before initializing Git, creating a remote, staging files or publishing code. Alternatively select an already published revision the user approves. ## Step 4: Upload Local Changes -Before launching, push any local changes so the remote reflects the code that should run: - -Review the changes, commit the user's intended pipeline files with a descriptive -message, and push the confirmed branch using the available Git tools. +Compare local changes with the selected remote revision. If the intended code is unpublished, stop and ask whether the user wants a separate commit/push task or a launch of the existing published revision. Only publish after explicit approval, staging only the approved files. If the working tree is clean and the local branch is in sync with the remote, skip this step. @@ -113,14 +123,14 @@ pipeline; it does not determine the user's inputs or output destination. ## Step 6: Monitor the Execution -`nextflow launch` returns a run URL on Nextflow Platform. Present this URL to the user so they can monitor progress in the Platform UI. +`nextflow launch` returns a run URL on Nextflow Platform. Retrieve the authoritative submitted workflow using discovered MCP operations and confirm its revision, parameters, compute environment and resume identity. Present the verified run identifier/URL and distinguish submission from successful completion. ## Critical Rules 1. **AUTHENTICATE first** — check `nextflow auth status` before attempting to launch. 2. **CONFIRM the compute environment** — always show the user the selected CE before launching. 3. **REQUIRE a remote Git repository** — the pipeline must be hosted on GitHub or a compatible Git host. If not, help the user set it up before launching. -4. **PUSH local changes first** — the launched run uses the remote code, so local edits must be committed and pushed. +4. **VERIFY the published revision** — use the approved remote code; obtain separate authorization before committing or pushing local changes. 5. **PASS the Git repository URL** to `nextflow launch`, not a local path. 6. **PIN the revision** — always use `-r` to target a specific branch, tag, or commit for reproducibility. 7. **USE cloud storage for `--outdir`** when the target CE runs on a cloud platform (s3://, gs://, az://). @@ -129,3 +139,8 @@ pipeline; it does not determine the user's inputs or output destination. ## MCP connection reference When a Seqera connection is missing or operation discovery is unclear, use the shared connection reference. Otherwise rely on the live tool descriptions and returned schemas. Read [MCP connection](references/seqera-mcp/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. diff --git a/skills/migrate-nextflow-code/SKILL.md b/skills/migrate-nextflow-code/SKILL.md index f7de98b..fe8017d 100644 --- a/skills/migrate-nextflow-code/SKILL.md +++ b/skills/migrate-nextflow-code/SKILL.md @@ -61,3 +61,10 @@ When CLI boolean flags arrive with the wrong type or do not toggle under strict ## Nextflow 25.04 compatibility reference When targeting 25.04 or diagnosing compatibility across that release, use its changelog and scanners without assuming 26.x features. Read [25.04 compatibility](references/nf-migrate-25-04/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. + +When editing an nf-core project, read [nf-core safety](../build-nextflow-pipeline/references/nf-core-safety.md); basic safe edits do not require the optional maintenance pack. diff --git a/skills/migrate-nextflow-code/references/nextflow-26-syntax/README.md b/skills/migrate-nextflow-code/references/nextflow-26-syntax/README.md index d34fe9e..9c06629 100644 --- a/skills/migrate-nextflow-code/references/nextflow-26-syntax/README.md +++ b/skills/migrate-nextflow-code/references/nextflow-26-syntax/README.md @@ -264,7 +264,7 @@ matching the baseline): 4. **Static types** — enable `nextflow.enable.types` one script at a time, leaves first (local modules → subworkflows → workflows → `main.nf`). Shared nf-core component files are owned upstream: do not rewrite them - in place (see `maintain-nf-core-pipeline`) — call them from typed code or + in place (see `nextflow-nf-core:maintain-nf-core-pipeline`) — call them from typed code or vendor a project-owned copy with a note, and say which you chose. 5. **Tuples → records** — the riskiest stage. Migrate one channel family at a time (e.g. the reads channel end-to-end, then the BAM channel), not one @@ -330,7 +330,7 @@ nextflow inspect 2>&1 - [boolean parameter compatibility](../nf-v2-boolean-params/README.md) — read the boolean compatibility reference when the task also involves a flag that is not toggling; otherwise keep the syntax investigation scoped to the observed parser errors. - `nf-pipeline-design` — typed process/workflow rules and the workflow `output {}` block in new code -- `maintain-nf-core-pipeline` — when the pipeline being migrated is an nf-core pipeline (template sync and module updates come first) +- `nextflow-nf-core:maintain-nf-core-pipeline` — when the pipeline being migrated is an nf-core pipeline (template sync and module updates come first) - `nf-test` / [nf-test failure repair](../../../nf-test/references/repair-nf-test/README.md) — regression tests between migration stages ## References diff --git a/skills/nextflow-config/SKILL.md b/skills/nextflow-config/SKILL.md index ba438cc..e1fbcd1 100644 --- a/skills/nextflow-config/SKILL.md +++ b/skills/nextflow-config/SKILL.md @@ -325,3 +325,8 @@ When generating a config: | `profiles` | Named config profiles | For the complete list of options in each scope, load the `config-options.md` reference. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. diff --git a/skills/nextflow-schema/SKILL.md b/skills/nextflow-schema/SKILL.md index 28de469..0a9f972 100644 --- a/skills/nextflow-schema/SKILL.md +++ b/skills/nextflow-schema/SKILL.md @@ -340,3 +340,8 @@ When deriving parameters from scripts, notebooks, papers or CLI documentation, p ## Legacy schema migration When upgrading nf-validation or draft-07 schemas, preserve validation, samplesheet tuple shape, help behavior and representative execution. Read [schema migration](references/nf-schema-migration/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. diff --git a/skills/nf-pipeline-design/SKILL.md b/skills/nf-pipeline-design/SKILL.md index 5d910ec..083fff3 100644 --- a/skills/nf-pipeline-design/SKILL.md +++ b/skills/nf-pipeline-design/SKILL.md @@ -1,6 +1,8 @@ --- name: nf-pipeline-design description: > + Also use for output aggregation, collectFile headers, join cardinality, + grouping keys and null-handling correctness. Make sure to use this skill whenever you are designing, writing, reviewing, or refactoring a Nextflow DSL2 pipeline with a focus on STRUCTURE — the shape of `main.nf`, where subworkflows belong, when something is a module @@ -35,8 +37,8 @@ manages OAuth for the connected MCP server. When a structural decision depends on a non-structural one, chain to: -- `find-alternative-tools` — tool choice at a branch -- `search-existing-modules` — reuse vs author a module +- [tool comparison](../build-nextflow-pipeline/references/find-alternative-tools/README.md) — tool choice at a branch +- [module discovery](../build-nextflow-pipeline/references/search-existing-modules/README.md) — reuse vs author a module - [parameter triage](../nextflow-schema/references/triage-pipeline-parameters/README.md) — param schema before `main.nf` ## Canonical Nextflow baseline @@ -1286,3 +1288,14 @@ script: run_tool --input ${fasta} """ ``` + +## Output correctness playbook + +When aggregating, joining or grouping outputs, check headers, cardinality, keys and null handling. Read [output correctness](references/nextflow-output-patterns/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. + +When editing an nf-core project, read [nf-core safety](../build-nextflow-pipeline/references/nf-core-safety.md); basic safe edits do not require the optional maintenance pack. diff --git a/skills/nextflow-output-patterns/SKILL.md b/skills/nf-pipeline-design/references/nextflow-output-patterns/README.md similarity index 82% rename from skills/nextflow-output-patterns/SKILL.md rename to skills/nf-pipeline-design/references/nextflow-output-patterns/README.md index f8bae6e..4d8b00c 100644 --- a/skills/nextflow-output-patterns/SKILL.md +++ b/skills/nf-pipeline-design/references/nextflow-output-patterns/README.md @@ -1,20 +1,3 @@ ---- -name: nextflow-output-patterns -description: > - Use this skill when writing or reviewing any Nextflow workflow that - aggregates per-sample outputs into a combined file, joins channels with - a remainder mode, or groups tuples for per-group processing. Covers the - operator idioms — `collectFile`, `join`, `groupTuple`, channel-level - null handling — that determine whether a workflow's output is - *correct*, not just whether it *runs*. Trigger on phrases like - `collectFile`, `groupTuple`, `join`, channel aggregation, per-sample - merging, combined output files, metadata-keyed grouping, optional - tuple positions, and the broader category of "the workflow finishes - without error but the merged output is malformed." Pair with - migrate-nextflow-code (strict v2 syntax) and build-nextflow-pipeline - (high-level structure and module composition); this skill is specifically about - output-correctness idioms in the operator layer. ---- ## Using this skill @@ -24,7 +7,7 @@ pipeline, input data and execution environment from their request or current context. Use user-selected locations for files and results. Consult companion skills, bundled references and optional helpers by name when available. -For Seqera operations, read the [MCP connection](../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples +For Seqera operations, read the [MCP connection](../../../launch-workflow/references/seqera-mcp/README.md) connection reference. Any `platform_*` examples describe API operations. Discover their exact names and parameter schemas with `search_seqera_api`, then invoke `call_seqera_api` using those schemas. The host manages OAuth for the connected MCP server. diff --git a/skills/nf-test/SKILL.md b/skills/nf-test/SKILL.md index 2317660..b37d0c6 100644 --- a/skills/nf-test/SKILL.md +++ b/skills/nf-test/SKILL.md @@ -139,3 +139,8 @@ For failing suites, assertion errors or snapshot mismatches, read [nf-test failu ## Failure repair playbook When an existing nf-test fails, classify intentional contract change, regression, nondeterminism or infrastructure before editing code, assertions or snapshots. Read [nf-test failure repair](references/repair-nf-test/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. diff --git a/skills/repair-workflow/SKILL.md b/skills/repair-workflow/SKILL.md index af89554..6a4c0d0 100644 --- a/skills/repair-workflow/SKILL.md +++ b/skills/repair-workflow/SKILL.md @@ -92,8 +92,15 @@ Reread the test output, inspect the actual produced artifacts, compare expected - No shadow implementation or copy-back workaround was introduced. - The representative test passes, or any remaining limitation is reported precisely. -Use [registry composition](../build-nextflow-pipeline/references/create-workflow/README.md) for new workflows, run-module for a single registry module, [strict syntax compatibility](../migrate-nextflow-code/references/nextflow-26-syntax/README.md) for strict-syntax changes, and [nf-test failure repair](../nf-test/references/repair-nf-test/README.md) for test-specific failures. Consult repair-checklists.md when available. +Use [registry composition](../build-nextflow-pipeline/references/create-workflow/README.md) for new workflows, [native module execution](../build-nextflow-pipeline/references/run-module/README.md) for a single registry module, [strict syntax compatibility](../migrate-nextflow-code/references/nextflow-26-syntax/README.md) for strict-syntax changes, and [nf-test failure repair](../nf-test/references/repair-nf-test/README.md) for test-specific failures. Consult repair-checklists.md when available. ## Static diagnostics playbook When the request concerns lint, config validation, compilation or why a pipeline will not start, use static diagnostics and honor whether the user requested diagnosis or repair. Read [static diagnostics](references/nf-debug/README.md) before proceeding. + + +## Optional specialist work + +For infrastructure setup, nf-core maintenance/analysis, plugin development or broad provenance work, read [optional pack handoffs](../build-nextflow-pipeline/references/optional-packs.md). Check available namespaced skills first; if the pack is absent, explain how to explicitly install/enable it and stop that specialist task. Ordinary debugging and launch/resume remain in core. + +When editing an nf-core project, read [nf-core safety](../build-nextflow-pipeline/references/nf-core-safety.md); basic safe edits do not require the optional maintenance pack. diff --git a/sources.json b/sources.json index e4e501c..b6c008e 100644 --- a/sources.json +++ b/sources.json @@ -1,64 +1,36 @@ { "portal_commit": "684d343e75ec6437d58c3e85279a8031384f3b62", "files": [ - { - "path": "skills/audit-conversion-readiness/SKILL.md", - "source": "portal/backend/src/skills/audit-conversion-readiness/SKILL.md", - "source_sha256": "c03ff0e0755129fb718f8d7d45dec4b222661c9c5e3af91145deab166907de29", - "bundled_sha256": "1951c0aaeeadfcd1a81baa76332ae374679c8bd5cdac26eda43ecbcc562a1362", - "override": true - }, - { - "path": "skills/audit-conversion-readiness/references/reference-patterns.md", - "source": "portal/backend/src/skills/audit-conversion-readiness/references/reference-patterns.md", - "source_sha256": "971a544370fa161400fa5c7f1a156abf2ae7c995f40d42ea4b8593b56de011ec", - "bundled_sha256": "a8e41a1ab262564941c6f217719c976d9180717efebca615aefcd9fa57391fa7", - "override": false - }, - { - "path": "skills/audit-conversion-readiness/references/report-template.md", - "source": "portal/backend/src/skills/audit-conversion-readiness/references/report-template.md", - "source_sha256": "b92c40dc2d4d18660761f7e38affd2183edcfd9d6245922bfe01f12ea3aefbff", - "bundled_sha256": "3656852fd045af27f5fc973b82e65bd8e13fd2f8c4f150b652b2adbfdd63f1ca", - "override": false - }, - { - "path": "skills/audit-conversion-readiness/references/tool-availability.md", - "source": "portal/backend/src/skills/audit-conversion-readiness/references/tool-availability.md", - "source_sha256": "be177bc6723e1612ed788436e0109560c1993345abb3ff1967da6c75c40e577b", - "bundled_sha256": "4e7ff003fe93330f1c96315e93567033998e295ef7d2b086ecd9c7802407cedb", - "override": true - }, { "path": "skills/build-nextflow-pipeline/SKILL.md", "source": "portal/backend/src/skills/build-nextflow-pipeline/SKILL.md", "source_sha256": "4dcc9dcaa19a74f8b9d05272271b5a55317ca8fd0e3ca11b3eb0edb43fe4dcad", - "bundled_sha256": "65d44a56973b99258a081a5fd58f4a3a978cdc11bfa198fd60342b7bec42455a", + "bundled_sha256": "6a948673d305a64eb07628ddb26f742cfa9d1a8d823572f03629e7798ada674b", "override": true }, { - "path": "skills/ce-credentials-setup/SKILL.md", + "path": "packs/nextflow-platform/skills/ce-credentials-setup/SKILL.md", "source": "portal/backend/src/skills/ce-credentials-setup/SKILL.md", "source_sha256": "179ed50da55eb509086eaf9e3228d063bd4d8334c0f8fff38c0f31e0e327e4e9", - "bundled_sha256": "f08f46ce58afa13ca971bd974578a388fa6e86851b8263ce2c1db5acb34e27e1", + "bundled_sha256": "658221450e37b494ec113152c290c5f045e6fe6dac092855c1ec224d45177af3", "override": true }, { - "path": "skills/ce-credentials-setup/references/aws-batch.md", + "path": "packs/nextflow-platform/skills/ce-credentials-setup/references/aws-batch.md", "source": "portal/backend/src/skills/ce-credentials-setup/references/aws-batch.md", "source_sha256": "0b72204b432f9c6a9f8ac476339a0639a300f137c83c362553a20deb426dba8f", "bundled_sha256": "93cf12538472e936f82267f8756a390f5d472c0069f33d851b4d8653b8f617f4", "override": true }, { - "path": "skills/ce-credentials-setup/references/kubernetes.md", + "path": "packs/nextflow-platform/skills/ce-credentials-setup/references/kubernetes.md", "source": "portal/backend/src/skills/ce-credentials-setup/references/kubernetes.md", "source_sha256": "1b55a04577e070016fec281df80294ccdc9e738485ce3fd3b82b02502d02af65", "bundled_sha256": "2cf64d58f6ab3df54b20133b005799245e15d79b104396af56c285add173be85", "override": true }, { - "path": "skills/ce-credentials-setup/references/seqera-compute.md", + "path": "packs/nextflow-platform/skills/ce-credentials-setup/references/seqera-compute.md", "source": "portal/backend/src/skills/ce-credentials-setup/references/seqera-compute.md", "source_sha256": "b76087e0b06de0984c3f22228846b19dc3561bbba27fd18c1162fe27fab78752", "bundled_sha256": "b1e39e794db10b38beb6079b7d82ee49c2c302f0480b676d06fa9ce0caebd1ac", @@ -68,21 +40,21 @@ "path": "skills/create-container/SKILL.md", "source": "portal/backend/src/skills/create-container/SKILL.md", "source_sha256": "7e87a45b6665d9cb282f7f9c145e688cf57affd6e95d84a61b8ce993fc811a57", - "bundled_sha256": "b645a0dd1b55e6e89a968e0644b04201d7d93dc05c1572c1d4e695b25cf15b2a", + "bundled_sha256": "cac969ad55e8f49277176641397305984d53016de69af41ff20dfeb7ae1838b2", "override": true }, { "path": "skills/debug-local-run/SKILL.md", "source": "portal/backend/src/skills/debug-local-run/SKILL.md", "source_sha256": "dc28ac095ffdbc4e4b798d1edf132edd7090e2f96508fdc7ecaded99074e9ba2", - "bundled_sha256": "cfaa0aadd28daa4781fad9df809f6160c2facd263bde274c7a8f6cdf08f505fb", + "bundled_sha256": "63eec54192423b368937d1684a16a1a9bc42679451991c4b109990f7bed0f951", "override": true }, { "path": "skills/debug-seqera-failed-run/SKILL.md", "source": "portal/backend/src/skills/debug-seqera-failed-run/SKILL.md", "source_sha256": "6825762051ab014d6b3fa6a8a4db12e79333a00e9cb0a746659167181c8b93a3", - "bundled_sha256": "1dff52c74077afc3b3d18c02dec83e5ccc46102c1b875a569579861f9adaa985", + "bundled_sha256": "62d42c307708f6f6586164f4ae18f9a55abd5da634980c8bc1b18fe99c2e1a58", "override": true }, { @@ -128,87 +100,38 @@ "override": false }, { - "path": "skills/find-alternative-tools/SKILL.md", - "source": "portal/backend/src/skills/find-alternative-tools/SKILL.md", - "source_sha256": "b3acbc1417255d5b26b9058d7b80fff92a1b732d218fd1b043e636fa26e223b1", - "bundled_sha256": "a3afb0b68ba4638f9ff0b6d2b27588a627040bb6b04e80e07d275c2ec65e7d35", - "override": true - }, - { - "path": "skills/maintain-nf-core-pipeline/SKILL.md", + "path": "packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/SKILL.md", "source": "portal/backend/src/skills/maintain-nf-core-pipeline/SKILL.md", "source_sha256": "4ab1ec7a1ad95f4e622efe4e7f56eec650e70f6f62ebe087639be82d000c837c", - "bundled_sha256": "3de0db5f48b81c4db6d70a3185651ecb425f99b051eb984e9fe8b7bb6df2c837", + "bundled_sha256": "6cc4ed1b9b7f004c30d15b13d253260f427a6141f5637accdee23cca40dc47db", "override": true }, { - "path": "skills/maintain-nf-core-pipeline/references/nf-core-conventions.md", + "path": "packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md", "source": "portal/backend/src/skills/maintain-nf-core-pipeline/references/nf-core-conventions.md", "source_sha256": "fee5073d8241a52fc24e38d60f979b1a8a49e665703d2800f3c1e7e5bd088878", - "bundled_sha256": "30fd736ccf1808f1ffa9d813aa0b490d41291c98772eafb6a5379c4a03a2a7dd", + "bundled_sha256": "226ad667d7c42f7438d5ff30afe1a5dd318079139ee040d1cecc6e89ce4df096", "override": true }, { - "path": "skills/maintain-nf-core-pipeline/references/template-merges/README.md", + "path": "packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/README.md", "source": "portal/backend/src/skills/maintain-nf-core-pipeline/references/template-merges/README.md", "source_sha256": "cd226cb30894f9242b0230115445b7e01f514c55551c14835a03581fd1ecff2b", "bundled_sha256": "ab13b25534c79838d127d78572270a43f9e8c473bc70103b52e23a456d18dc8a", "override": false }, { - "path": "skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md", + "path": "packs/nextflow-nf-core/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md", "source": "portal/backend/src/skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md", "source_sha256": "743295a75fea1c54adc6e93c8b479012a705beb0d74a599c2262b417f0cf415c", - "bundled_sha256": "79f3cb51a5f1b9062a15423ea87d6278085694d5047bd5628b83ac04586b18ac", + "bundled_sha256": "ac54e63514cebc42b9d36438b7c0a8caf62866cfd965c10e271bb54368c8b189", "override": true }, - { - "path": "skills/migrate-from-snakemake/SKILL.md", - "source": "portal/backend/src/skills/migrate-from-snakemake/SKILL.md", - "source_sha256": "ad385af7b45a52955ba7b7b924efbb63362a98e20998ec51558e1146ab1b4880", - "bundled_sha256": "118f2d75d609f3e0020136964cae60508cd5255f8c84c07a8ecf588f817da6e4", - "override": true - }, - { - "path": "skills/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md", - "source": "portal/backend/src/skills/migrate-from-snakemake/references/nextflow-conda-troubleshooting.md", - "source_sha256": "21c17c71e82bb6393aaed4757b1f229b03c88f44a7713de9ad0c738a0442e433", - "bundled_sha256": "ee962d892a202a056105dbc68267a5a10fc62e61c9d460bfcf36224b51511062", - "override": false - }, - { - "path": "skills/migrate-from-snakemake/references/snakemake-nextflow-playbook.md", - "source": "portal/backend/src/skills/migrate-from-snakemake/references/snakemake-nextflow-playbook.md", - "source_sha256": "de986ee318ad4be3422502f696f26f6d6788d145a4c6e246cb46067656788b11", - "bundled_sha256": "9271fc3d0cffe03a184749692bf41d5486ddcfc323d401870bc60e442211cb43", - "override": false - }, - { - "path": "skills/migrate-from-snakemake/references/snakemake-rules-core.md", - "source": "portal/backend/src/skills/migrate-from-snakemake/references/snakemake-rules-core.md", - "source_sha256": "dbf9d07b324db17b8123c59d2ed44083ecfc2247bcb37e18d07b58204c165bfd", - "bundled_sha256": "28c749e78e17db095727170a8e23f2566f064d3ce651b149b593508360e257b1", - "override": false - }, - { - "path": "skills/migrate-from-snakemake/references/snakemake-testing-unit-tests.md", - "source": "portal/backend/src/skills/migrate-from-snakemake/references/snakemake-testing-unit-tests.md", - "source_sha256": "9857ea5f89bb7d2376a2eaeead46305a0f1e45cf5a88691c368692fc17a4477a", - "bundled_sha256": "bd5acdddd51ad1bc730ad78bd1b61520c94f2ef9de4697d1c36f3473a8fff13e", - "override": false - }, - { - "path": "skills/migrate-from-snakemake/references/snakemake-writing-workflows.md", - "source": "portal/backend/src/skills/migrate-from-snakemake/references/snakemake-writing-workflows.md", - "source_sha256": "551afd0c162468fc427d38e0bebc2eaacf166780f21779b1a76f9388fe1d5814", - "bundled_sha256": "786ebe625b8d619affb75be8f942e5e4c64645a52be5e268d01b00f732484313", - "override": false - }, { "path": "skills/nextflow-config/SKILL.md", "source": "portal/backend/src/skills/nextflow-config/SKILL.md", "source_sha256": "1c421137313d594b23128d5bb74768ba8c68617f23f612f9961292a359f4b8dd", - "bundled_sha256": "2aff5b7f9ce1eb14e378bb786de522c12b56bafd2c7b04d969bcf98276d0be8f", + "bundled_sha256": "c087a45be01557d19416eb240d237fe668d56ae5d247aed0fc5042eb0db4a548", "override": true }, { @@ -226,24 +149,17 @@ "override": true }, { - "path": "skills/nextflow-history/SKILL.md", + "path": "packs/nextflow-provenance/skills/nextflow-history/SKILL.md", "source": "portal/backend/src/skills/nextflow-history/SKILL.md", "source_sha256": "4f2ce1b1d39236f1f5b1d7de1ae07d3324b2b8cc32c79e3c6821f43cd2e09bd4", - "bundled_sha256": "4d7db39e87e790db250b8aeb504350faec2d3b3d0d3491b979ee55edadb22a2a", - "override": true - }, - { - "path": "skills/nextflow-output-patterns/SKILL.md", - "source": "portal/backend/src/skills/nextflow-output-patterns/SKILL.md", - "source_sha256": "b8ee43fb09ae92ddf90b7b4ea9517b4660e297879804c8a51c1988765017df72", - "bundled_sha256": "9ce001226ba2c0a5217ba2b78bdadd18727d78abb3ad3203e979f57230a9d9a5", + "bundled_sha256": "8dfdc0a483ef7ea69a1ac0d93f1e88f46bbd619f6c062d32d935f6016c9e94c7", "override": true }, { "path": "skills/nextflow-schema/SKILL.md", "source": "portal/backend/src/skills/nextflow-schema/SKILL.md", "source_sha256": "52e37b4ae0418b3ed7e8277b184efcc9fe2e67e2a877dd6c5df0b92203c91345", - "bundled_sha256": "a86c1312969e75f8b996c2ceef8d5b6b54c5675cbfa998a363a6c740ff56ded8", + "bundled_sha256": "6d8c12ff6d2419c16928c38c8e00c4bb9928afabe5cdb0486c0fa7520d866bea", "override": true }, { @@ -268,31 +184,17 @@ "override": false }, { - "path": "skills/nf-data-lineage/SKILL.md", + "path": "packs/nextflow-provenance/skills/nf-data-lineage/SKILL.md", "source": "portal/backend/src/skills/nf-data-lineage/SKILL.md", "source_sha256": "81f88126cf85d2da22f03f7f5ae3c38256b63cccc5350cfc7348e55631ca92a7", - "bundled_sha256": "217cf839f27edd53e9b8e6fd3c1658c13a8c8745f00131d0ca409b91786edb06", + "bundled_sha256": "175450ad1b0f9873b1588b5c2ac5bf87891d8b7ada679a7325c0b2be57053e7d", "override": true }, - { - "path": "skills/nf-docker-scripts/SKILL.md", - "source": "portal/backend/src/skills/nf-docker-scripts/SKILL.md", - "source_sha256": "867fbfd0d732efc9655df1e025e89a608f049bf2397b057a38fcfd1af266b249", - "bundled_sha256": "03cf2260d63b6266813a39074743e369170ad664ab598581c900e564d0c2d1f8", - "override": true - }, - { - "path": "skills/nf-docker-scripts/references/script-strategies-deep-dive.md", - "source": "portal/backend/src/skills/nf-docker-scripts/references/script-strategies-deep-dive.md", - "source_sha256": "5adc413d42b2f962602f48e6482861cda160071cc3c0368c778ec7ae5f2ced11", - "bundled_sha256": "d2c6232dec34c748662d945d575cba2ca7475ae8f090904bb4dc426e313539ba", - "override": false - }, { "path": "skills/nf-pipeline-design/SKILL.md", "source": "portal/backend/src/skills/nf-pipeline-design/SKILL.md", "source_sha256": "580d7f415a3a267fc2bd23da92848281b4cc32974a14c978b3395bdcfa6a4645", - "bundled_sha256": "c399ca5043d70a869049e2509a55ae254e9f39ca22a235ce47c1cdd55e606b3d", + "bundled_sha256": "cebd43275aef5334b7b72b56e759b5e1e9bad4eeed8ec413690235b2cd2deed3", "override": true }, { @@ -464,24 +366,17 @@ "override": false }, { - "path": "skills/nf-plugin-development/SKILL.md", + "path": "packs/nextflow-plugins/skills/nf-plugin-development/SKILL.md", "source": "portal/backend/src/skills/nf-plugin-development/SKILL.md", "source_sha256": "5a328e82652bbe4d0dfc3afdc3877379ce54e1fea7258b6bbf432692a31ee117", - "bundled_sha256": "f516302bd674f1642291569c8daf20e3fb10abd4d740716b55c2c0c69b2858f2", - "override": true - }, - { - "path": "skills/nf-plugin-legacy-migration/SKILL.md", - "source": "portal/backend/src/skills/nf-plugin-legacy-migration/SKILL.md", - "source_sha256": "635d3c3ad2fb29f77cf4bea08cbea5267b636d45aa697d05302a1081d5545c97", - "bundled_sha256": "20087fc58d5543faf735b18dee7fe9b16ff4feb541c79edaf0e464a251d2c9a4", + "bundled_sha256": "3d0a304efea9406afcb31531b8ff0b4eb956dbb922717ea90bbe0d909ca5c46e", "override": true }, { "path": "skills/nf-test/SKILL.md", "source": "portal/backend/src/skills/nf-test/SKILL.md", "source_sha256": "87865ca1eac374c3a0425abae85401a03a477ae0a78db353eb3742c08ff4fc96", - "bundled_sha256": "21d2ffd2853a4e3ba8b8a6eebc7a2616f1f04edfb15f3b7701daa6ec83e72d76", + "bundled_sha256": "30bca54b9cc365e7799ffd2cc89ef4c4633b3900e359bc4e20e9e18ac5a418ba", "override": true }, { @@ -523,7 +418,7 @@ "path": "skills/repair-workflow/SKILL.md", "source": "portal/backend/src/skills/repair-workflow/SKILL.md", "source_sha256": "43567947449b6dcd44c34bded2a44c93826d42fd703c71576fdca3780e39d72a", - "bundled_sha256": "eb5e0fb4c5f490fd94adfa0563ecf98984fcf2377cddb213df941a6fb396262d", + "bundled_sha256": "c955070e9a18291a237f7c443a785824fd7eed54f7867716b1e5ba5f3ddce6ab", "override": true }, { @@ -534,175 +429,168 @@ "override": true }, { - "path": "skills/search-existing-modules/SKILL.md", - "source": "portal/backend/src/skills/search-existing-modules/SKILL.md", - "source_sha256": "73ab4e956a3bddd4382a8d74911963a8c51a72abcd3ff8a7fd0d49bd8ffd53a9", - "bundled_sha256": "c75b8a5342dea17c076dff23ab44c927dd32d399d203d2059c3b7a74449c3232", - "override": true - }, - { - "path": "skills/seqera-data-links/SKILL.md", + "path": "packs/nextflow-platform/skills/seqera-data-links/SKILL.md", "source": "portal/backend/src/skills/seqera-data-links/SKILL.md", "source_sha256": "1ac21b9aa3cc01ab4c05497675b439da3eebe85b17ceb326e953a586681a04fb", - "bundled_sha256": "4bffc8f64b60cfe29d330d01a6044f9598902ab8280e31561a75d0c7e0039ac5", + 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"skills/install-nextflow/SKILL.md", "skills/launch-workflow/SKILL.md", "skills/launch-workflow/references/seqera-mcp/README.md", - "skills/maintain-nf-core-pipeline/SKILL.md", - "skills/maintain-nf-core-pipeline/references/nf-core-conventions.md", - "skills/maintain-nf-core-pipeline/references/template-merges/tools-4_0.md", - "skills/migrate-from-snakemake/SKILL.md", "skills/migrate-nextflow-code/SKILL.md", "skills/migrate-nextflow-code/references/nextflow-26-syntax/README.md", "skills/migrate-nextflow-code/references/nf-migrate-25-04/README.md", @@ -1173,30 +1280,20 @@ "skills/migrate-nextflow-code/references/nf-migrate-25-04/scripts/find_deprecated_patterns.py", "skills/migrate-nextflow-code/references/nf-migrate-25-04/scripts/find_shell_blocks.py", "skills/migrate-nextflow-code/references/nf-v2-boolean-params/README.md", + "skills/migrate-nextflow-code/references/static-typing.md", "skills/nextflow-config/SKILL.md", "skills/nextflow-config/references/config-options.md", - "skills/nextflow-development/SKILL.md", - "skills/nextflow-history/SKILL.md", - "skills/nextflow-history/references/nf-run-history/README.md", - "skills/nextflow-output-patterns/SKILL.md", "skills/nextflow-schema/SKILL.md", "skills/nextflow-schema/references/nf-schema-migration/README.md", "skills/nextflow-schema/references/nf-schema-migration/references/migration-guide.md", "skills/nextflow-schema/references/triage-pipeline-parameters/README.md", - "skills/nf-data-lineage/SKILL.md", - "skills/nf-docker-scripts/SKILL.md", "skills/nf-pipeline-design/SKILL.md", - "skills/nf-plugin-development/SKILL.md", - "skills/nf-plugin-legacy-migration/SKILL.md", + "skills/nf-pipeline-design/references/nextflow-output-patterns/README.md", "skills/nf-test/SKILL.md", "skills/nf-test/references/repair-nf-test/README.md", "skills/repair-workflow/SKILL.md", "skills/repair-workflow/references/nf-debug/README.md", - "skills/repair-workflow/references/repair-checklists.md", - "skills/run-module/SKILL.md", - "skills/search-existing-modules/SKILL.md", - "skills/seqera-data-links/SKILL.md", - "skills/seqerakit/SKILL.md" + "skills/repair-workflow/references/repair-checklists.md" ], "consolidated_skills": [ { @@ -1250,7 +1347,75 @@ { "from": "seqera-mcp", "to": "launch-workflow" + }, + { + "from": "migrate-from-snakemake", + "to": "build-nextflow-pipeline" + }, + { + "from": "audit-conversion-readiness", + "to": "build-nextflow-pipeline" + }, + { + "from": "search-existing-modules", + "to": "build-nextflow-pipeline" + }, + { + "from": "run-module", + "to": "build-nextflow-pipeline" + }, + { + "from": "find-alternative-tools", + "to": "build-nextflow-pipeline" + }, + { + "from": "install-nextflow", + "to": "build-nextflow-pipeline" + }, + { + "from": "nextflow-output-patterns", + "to": "nf-pipeline-design" + }, + { + "from": "nf-docker-scripts", + "to": "create-container" + }, + { + "from": "nf-plugin-legacy-migration", + "to": "nf-plugin-development" } - ] + ], + "skill_pack_plan_sha256": "4548b4e68d87cafeb8f2ad8d754c99f7ca230be35a2fb87b6bde78a709db2b0c", + "skill_packs": { + "nextflow": [ + "build-nextflow-pipeline", + "nf-pipeline-design", + "repair-workflow", + "debug-local-run", + "debug-seqera-failed-run", + "nf-test", + "migrate-nextflow-code", + "nextflow-schema", + "nextflow-config", + "create-container", + "launch-workflow" + ], + "nextflow-platform": [ + "ce-credentials-setup", + "seqera-data-links", + "seqerakit" + ], + "nextflow-nf-core": [ + "nextflow-development", + "maintain-nf-core-pipeline" + ], + "nextflow-plugins": [ + "nf-plugin-development" + ], + "nextflow-provenance": [ + "nextflow-history", + "nf-data-lineage" + ] + } } } diff --git a/tools/build_skill_packs.py b/tools/build_skill_packs.py new file mode 100644 index 0000000..32a2071 --- /dev/null +++ b/tools/build_skill_packs.py @@ -0,0 +1,223 @@ +#!/usr/bin/env python3 +"""Generate an eleven-skill core and opt-in plugins from the curated catalog. + +Run after the original consolidation and manifest generation. Re-import upstream +content to change a completed partition; replay validates it without moving files. +""" + +import argparse +import hashlib +import json +import os +import re +import shutil +import subprocess +import sys +from pathlib import Path + +PLAN = Path(__file__).with_name("skill_packs.json") +LINK = re.compile(r"(\[[^\]]*\]\()([^\s)]+)\)") + + +def write_pack_json(path: Path, value: dict) -> None: + path.parent.mkdir(parents=True, exist_ok=True) + path.write_text(json.dumps(value, indent=2, ensure_ascii=False) + "\n") + + +def validate_pack_files(root: Path, sources: dict) -> None: + for entry in sources["files"]: + path = root / entry["path"] + if not path.is_file(): + raise ValueError(f"missing bundled file: {entry['path']}") + if hashlib.sha256(path.read_bytes()).hexdigest() != entry["bundled_sha256"]: + raise ValueError(f"bundled file changed: {entry['path']}; re-import before rebuilding packs") + + +def build_skill_packs(root: Path, plan: dict, assets: Path, version: str | None = None) -> None: + assignments = [(name, "nextflow") for name in plan["core"]] + assignments += [(name, pack["name"]) for pack in plan["packs"] for name in pack["skills"]] + owners = dict(assignments) + if len(owners) != len(assignments): + raise ValueError("skill assigned more than once in pack plan") + manifest = json.loads((root / ".claude-plugin/plugin.json").read_text()) + if version: + manifest["version"] = version + signature = hashlib.sha256(json.dumps({"plan": plan, "version": manifest["version"]}, sort_keys=True).encode()).hexdigest() + sources = json.loads((root / "sources.json").read_text()) + curation = sources["claude_curation"] + if curation.get("skill_pack_plan_sha256"): + if curation["skill_pack_plan_sha256"] != signature: + raise ValueError("skill pack plan changed; re-import before rebuilding packs") + validate_pack_files(root, sources) + validate_pack_inventory(root, plan) + subprocess.run([sys.executable, "-I", str(Path(__file__).with_name("check_sources.py")), "--root", str(root)], check=True) + return + if (root / "packs").exists(): + raise ValueError("partial skill pack output; re-import before rebuilding packs") + fold_plan = None + if plan.get("consolidations"): + fold_plan = assets / plan["consolidations"] + folds = json.loads(fold_plan.read_text()) + removed = {fold["from"] for group in folds["groups"] for fold in group["folds"]} + else: + removed = set() + live = {p.parent.name for p in (root / "skills").glob("*/SKILL.md")} + if live not in (set(owners), set(owners) | removed): + raise ValueError(f"skill pack inventory mismatch: unexpected={sorted(live - set(owners) - removed)}, missing={sorted(set(owners) - live)}") + if fold_plan: + subprocess.run([sys.executable, "-I", str(Path(__file__).with_name("consolidate_skills.py")), "--root", str(root), "--plan", str(fold_plan)], check=True) + sources = json.loads((root / "sources.json").read_text()) + curation = sources["claude_curation"] + old_paths = [p for p in (root / "skills").rglob("*") if p.is_file()] + recorded = {entry["path"] for entry in sources["files"]} + for path in old_paths: + relative = str(path.relative_to(root)) + if relative not in recorded: + digest = hashlib.sha256(path.read_bytes()).hexdigest() + sources["files"].append({"path": relative, "source": "imported-package/" + relative, + "source_sha256": digest, "bundled_sha256": digest, + "note": "No upstream provenance entry was provided; hash records imported bytes."}) + mapped = {} + for path in old_paths: + relative = path.relative_to(root / "skills") + owner = owners[relative.parts[0]] + base = root if owner == "nextflow" else root / "packs" / owner + mapped[path.resolve()] = base / "skills" / relative + for pack in plan["packs"]: + base = root / "packs" / pack["name"] + (base / "skills").mkdir(parents=True) + for name in pack["skills"]: + shutil.move(str(root / "skills" / name), base / "skills" / name) + + # Resolve in the original tree, then rewrite using each installed plugin root. + # Filesystem links across cache roots become explicit namespaced skill handoffs. + for old, new in mapped.items(): + if new.suffix != ".md": + continue + skill = old.relative_to(root / "skills").parts[0] + owner = owners[skill] + base = root if owner == "nextflow" else root / "packs" / owner + + def relocate_link(match): + target, separator, anchor = match.group(2).partition("#") + if not target or target.startswith(("/", "<")) or re.match(r"[a-zA-Z][\w+.-]*:", target): + return match.group() + original = (old.parent / target).resolve() + destination = mapped.get(original, original) + if destination.is_relative_to(base) and not (owner == "nextflow" and destination.is_relative_to(root / "packs")): + return f"{match.group(1)}{Path(os.path.relpath(destination, new.parent)).as_posix()}{separator}{anchor})" + if original == (root / "skills/launch-workflow/references/seqera-mcp/README.md").resolve(): + connection = base / "references/mcp-connection.md" + return f"{match.group(1)}{Path(os.path.relpath(connection, new.parent)).as_posix()})" + if original.is_relative_to(root / "skills"): + name = original.relative_to(root / "skills").parts[0] + label = match.group(1)[1:-2] + return f"{label}: consult `{owners[name]}:{name}` and its matching reference (requires that plugin to be enabled)" + raise ValueError(f"resource escapes plugin root: {new.relative_to(root)} -> {target}") + + text = LINK.sub(relocate_link, new.read_text()) + for name, pack_owner in owners.items(): + if pack_owner == "nextflow": + continue + pattern = rf"`{re.escape(name)}`|(? None: + for name, expected in [("nextflow", plan["core"])] + [(p["name"], p["skills"]) for p in plan["packs"]]: + base = root if name == "nextflow" else root / "packs" / name + actual = {p.parent.name for p in (base / "skills").glob("*/SKILL.md")} + if actual != set(expected): + raise ValueError(f"skill pack inventory mismatch for {name}: {sorted(actual)}") + + +def main() -> None: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--root", type=Path, default=Path(__file__).resolve().parent.parent) + parser.add_argument("--plan", type=Path, default=PLAN) + parser.add_argument("--version", help="release version for all generated manifests; defaults to core manifest") + args = parser.parse_args() + build_skill_packs(args.root.resolve(), json.loads(args.plan.read_text()), args.plan.parent, args.version) + + +if __name__ == "__main__": + main() diff --git a/tools/check_sources.py b/tools/check_sources.py index 7ed822b..e3e7abd 100644 --- a/tools/check_sources.py +++ b/tools/check_sources.py @@ -1,41 +1,101 @@ #!/usr/bin/env python3 -"""Verify that bundled files match the hashes recorded in sources.json and that manifests agree.""" +"""Verify bundled hashes, plugin inventories, versions and installed-root links.""" +import argparse import hashlib import json +import re import sys from pathlib import Path REPO = Path(__file__).resolve().parent.parent -def main() -> int: +def check_plugin_packages(root: Path) -> list[str]: errors = [] - - sources = json.loads((REPO / "sources.json").read_text()) + sources = json.loads((root / "sources.json").read_text()) + recorded = set() for entry in sources["files"]: - path = REPO / entry["path"] + relative = entry["path"] + if relative in recorded: + errors.append(f"duplicate bundled path: {relative}") + recorded.add(relative) + path = root / relative if not path.is_file(): - errors.append(f"missing bundled file: {entry['path']}") + errors.append(f"missing bundled file: {relative}") + elif hashlib.sha256(path.read_bytes()).hexdigest() != entry["bundled_sha256"]: + errors.append(f"hash mismatch: {relative}") + + marketplace = json.loads((root / ".claude-plugin/marketplace.json").read_text()) + listed = set() + for entry in marketplace["plugins"]: + name = entry["name"] + if name in listed: + errors.append(f"marketplace must list plugin {name} exactly once") + listed.add(name) + source = entry["source"] + base = (root / source).resolve() + if not base.is_relative_to(root.resolve()): + errors.append(f"plugin source escapes marketplace: {source}") continue - digest = hashlib.sha256(path.read_bytes()).hexdigest() - if digest != entry["bundled_sha256"]: - errors.append(f"hash mismatch: {entry['path']}") - - plugin = json.loads((REPO / ".claude-plugin" / "plugin.json").read_text()) - marketplace = json.loads((REPO / ".claude-plugin" / "marketplace.json").read_text()) - entries = [p for p in marketplace["plugins"] if p["name"] == plugin["name"]] - if len(entries) != 1: - errors.append(f"marketplace must list plugin {plugin['name']} exactly once") - elif entries[0].get("version") != plugin["version"]: - errors.append(f"version mismatch: plugin.json {plugin['version']} vs marketplace {entries[0].get('version')}") - - for skill in sorted((REPO / "skills").iterdir()): - if skill.is_dir() and not (skill / "SKILL.md").is_file(): - errors.append(f"skill directory without SKILL.md: {skill.name}") + manifest = base / ".claude-plugin/plugin.json" + if not manifest.is_file(): + errors.append(f"missing plugin manifest: {source}") + continue + plugin = json.loads(manifest.read_text()) + if plugin["name"] != name or entry.get("version") != plugin.get("version"): + errors.append(f"name/version mismatch for {name}") + if base != root.resolve() and ((base / ".mcp.json").exists() or plugin.get("mcpServers")): + errors.append(f"optional plugin registers a duplicate MCP connection: {name}") + if base != root.resolve(): + local_manifest = base / "sources.json" + if not local_manifest.is_file(): + errors.append(f"missing installed-pack provenance: {name}") + else: + prefix = str(base.relative_to(root)) + "/" + expected_files = [{**e, "path": e["path"][len(prefix):]} for e in sources["files"] if e["path"].startswith(prefix)] + if json.loads(local_manifest.read_text())["files"] != expected_files: + errors.append(f"installed-pack provenance mismatch: {name}") + actual = set() + for skill in sorted((base / "skills").iterdir()): + if not skill.is_dir(): + continue + if not (skill / "SKILL.md").is_file(): + errors.append(f"skill directory without SKILL.md: {name}/{skill.name}") + actual.add(skill.name) + expected = sources["claude_curation"].get("skill_packs", {}).get(name) + if expected is not None and actual != set(expected): + errors.append(f"skill inventory mismatch for {name}") + for path in (base / "skills").rglob("*"): + if not path.is_file(): + continue + if str(path.relative_to(root)) not in recorded: + errors.append(f"unrecorded bundled file: {path.relative_to(root)}") + if path.suffix != ".md": + continue + for target in re.findall(r"\[[^\]]*\]\(([^\s)]+)\)", path.read_text()): + if target.startswith(("#", "/", "<")) or re.match(r"[a-zA-Z][\w+.-]*:", target): + continue + destination = (path.parent / target.partition("#")[0]).resolve() + if not destination.is_file(): + errors.append(f"missing local link: {path.relative_to(root)} -> {target}") + elif not destination.is_relative_to(base) or (base == root.resolve() and destination.is_relative_to(root / "packs")): + errors.append(f"link escapes installed plugin: {path.relative_to(root)} -> {target}") + expected_plugins = sources["claude_curation"].get("skill_packs", {}) + if expected_plugins and listed != set(expected_plugins): + errors.append("marketplace plugin inventory differs from generated partition") + return errors + +def main() -> int: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--root", type=Path, default=REPO) + args = parser.parse_args() + root = args.root.resolve() + errors = check_plugin_packages(root) for error in errors: print(f"error: {error}", file=sys.stderr) + sources = json.loads((root / "sources.json").read_text()) print(f"checked {len(sources['files'])} files, {len(errors)} error(s)") return 1 if errors else 0 diff --git a/tools/consolidate_skills.py b/tools/consolidate_skills.py index 9042432..7b7ab3e 100644 --- a/tools/consolidate_skills.py +++ b/tools/consolidate_skills.py @@ -151,10 +151,10 @@ def apply_consolidations(root: Path, plan: dict, assets: Path) -> None: edited.add(entry["path"]) entry["bundled_sha256"] = digest sources["files"] = list(entries.values()) - sources["claude_curation"]["consolidated_skills"] = [ - {"from": fold["from"], "to": fold["to"]} - for group in plan["groups"] for fold in group["folds"] - ] + consolidated = {item["from"]: item for item in sources["claude_curation"].get("consolidated_skills", [])} + consolidated.update({fold["from"]: {"from": fold["from"], "to": fold["to"]} + for group in plan["groups"] for fold in group["folds"]}) + sources["claude_curation"]["consolidated_skills"] = list(consolidated.values()) sources["claude_curation"]["edited_files"] = sorted(edited & entries.keys()) write_json(sources_path, sources) diff --git a/tools/core_skill_consolidations.json b/tools/core_skill_consolidations.json new file mode 100644 index 0000000..8fb0d2d --- /dev/null +++ b/tools/core_skill_consolidations.json @@ -0,0 +1,147 @@ +{ + "groups": [ + { + "folds": [ + { + "from": "migrate-from-snakemake", + "to": "build-nextflow-pipeline", + "label": "snakemake conversion", + "when": "When converting a Snakefile, preserve DAG, wildcard, scheduler and golden-output semantics.", + "heading": "Snakemake conversion playbook" + }, + { + "from": "audit-conversion-readiness", + "to": "build-nextflow-pipeline", + "label": "conversion readiness", + "when": "For an audit-only request, inventory and probe inputs, code and dependencies; stop with a blockers-first report without editing pipeline code.", + "heading": "Conversion readiness playbook" + }, + { + "from": "search-existing-modules", + "to": "build-nextflow-pipeline", + "label": "module discovery", + "when": "When selecting a tool implementation, return a verified reuse, vendor/adapt or write-new verdict.", + "heading": "Module discovery playbook" + }, + { + "from": "run-module", + "to": "build-nextflow-pipeline", + "label": "native module execution", + "when": "For a module-only request, inspect the module contract and run it natively on verified inputs; no wrapper workflow or construction phases are needed.", + "heading": "Native module execution playbook" + }, + { + "from": "find-alternative-tools", + "to": "build-nextflow-pipeline", + "label": "tool comparison", + "when": "For requested comparisons or a blocked selected tool, compare alternatives; implementation needs separate user approval.", + "heading": "Tool comparison playbook" + }, + { + "from": "install-nextflow", + "to": "build-nextflow-pipeline", + "label": "runtime setup", + "when": "For installation or upgrade help, check the selected release and operation first; ask before changing the environment.", + "heading": "Runtime setup playbook" + }, + { + "from": "nextflow-output-patterns", + "to": "nf-pipeline-design", + "label": "output correctness", + "when": "When aggregating, joining or grouping outputs, check headers, cardinality, keys and null handling.", + "heading": "Output correctness playbook" + }, + { + "from": "nf-docker-scripts", + "to": "create-container", + "label": "script packaging", + "when": "For script-placement questions, choose and verify staging or packaging without requiring a container build.", + "heading": "Script packaging playbook" + } + ], + "edits": [ + { + "path": "skills/build-nextflow-pipeline/SKILL.md", + "old": "description: >\n Plan and scaffold a new Nextflow DSL2 pipeline from source material —\n scripts, repositories, Jupyter/R notebooks, papers, or informal\n instructions. Drives the planning phases before any .nf code is written:\n mapping the data flow, critiquing it, shaping channels and metadata,\n scoping subworkflows, hunting for existing modules, and only then building\n containers and writing code. Use this skill whenever the user asks to\n \"build a pipeline\", \"compose registry modules\", \"port this to Nextflow\", \"turn this notebook/repo/script\n into a pipeline\", or otherwise wants to go from an existing body of work to\n a clean Nextflow pipeline. Pair with `nf-pipeline-design`, which owns the\n code-level rules (layout, main.nf, subworkflow/module shape); this skill\n owns the planning process that precedes them.", + "new": "description: >\n Build or convert Nextflow pipelines from scripts, notebooks, repositories\n or Snakemake workflows. Also use for read-only conversion readiness audits,\n discovering or directly running registry modules, requested tool comparisons,\n and Nextflow installation or upgrade help. Choose the bounded task path;\n only full pipeline construction uses the planning phases. Pair with\n nf-pipeline-design for code structure and output contracts.\n Route compute/credential setup to the optional nextflow-platform pack,\n nf-core analysis/maintenance to nextflow-nf-core, extension plugin work to\n nextflow-plugins, and broad run/cache/lineage analysis to nextflow-provenance.\n If a specialist is absent, name its pack from the nextflow-claude-plugin\n marketplace and ask the user to explicitly install/enable it; stop that task." + }, + { + "path": "skills/build-nextflow-pipeline/SKILL.md", + "old": "## Choose the construction path", + "new": "## Choose the requested task\n\nFor compute/credential setup, omics analysis/nf-core maintenance, extension plugin development or broad provenance work, read [optional pack handoffs](references/optional-packs.md) first. If the matching namespaced specialist is absent, name its pack, explain explicit installation/enablement and stop that specialist task. These requests do not enter construction phases.\n\nFor an audit-only request, use the conversion-readiness playbook and return its report without writing pipeline code. For module discovery or a single module run, use the matching playbook and stop with a reuse verdict or verified run result. For tool comparison or runtime setup, use only that playbook and stop at the requested answer or authorized environment change.\n\nThese bounded paths skip the full construction phases below. When delegating a helper task, supply the relevant playbook content rather than invoking a removed skill identity.\n\n## Choose the construction path" + }, + { + "path": "skills/migrate-from-snakemake/SKILL.md", + "old": "For the complete conventions (branches, edit policy, CLI commands), chain `maintain-nf-core-pipeline` and read its `nf-core-conventions.md`.", + "new": "For nf-core-safe editing, read [nf-core safety](../build-nextflow-pipeline/references/nf-core-safety.md). Template synchronization or upstream contribution is a separate optional maintenance task." + }, + { + "path": "skills/install-nextflow/SKILL.md", + "old": "2. If the installed version is **older than 26.04**, the user MUST upgrade — other Nextflow skills depend on it.\n3. Otherwise, propose an upgrade only if a newer version is available.", + "new": "2. Check whether the installed release supports the user's requested operation. Ordinary pipeline execution does not inherit the 26.04 minimum used by native module or launch commands.\n3. If the operation is unsupported, explain the minimum supported release and ask before upgrading; otherwise keep the existing installation unless the user requests an upgrade." + }, + { + "path": "skills/install-nextflow/SKILL.md", + "old": "# Install or Upgrade Nextflow", + "new": "# Install or Upgrade Nextflow\n\nAn installation-help request is not permission to change the environment. Confirm the target release, Java/runtime prerequisites and user's approval before any installer, package-manager command or self-update." + }, + { + "path": "skills/create-container/SKILL.md", + "old": "description: >\n Build, claim, or recommend a verified container for a bioinformatics tool —\n and prove it runs the intended command on representative test data before\n handing it off for module authoring. Make sure to use this skill whenever\n the user wants to containerize a tool, wrap a tool for a Nextflow module,\n set up Wave for a custom package stack, pin a Bioconda/conda-forge\n environment, or unblock a \"this tool's dependencies are weird\" problem.\n Trigger phrases include \"containerize X\", \"I need an image for Y\",\n \"set up Wave for Z\", \"build a conda env for this tool\", \"verify this\n container works on test input\", \"what container does need\",\n \"wrap for a Nextflow module\", \"fix this conda solve\". Follows a\n build → run-test-input → iterate loop and returns a structured handoff\n (verified image reference + working command). Do not author the Nextflow\n module here — that belongs in `build-nextflow-pipeline` after verification.", + "new": "description: >\n Create and verify containers for Nextflow tools using Wave or the selected\n runtime. Also use for choosing where process scripts live, helper-command\n staging, templates and image packaging. Script-placement advice does not\n require building an image. Verify the requested command and representative\n outputs before claiming a container works." + }, + { + "path": "skills/nf-pipeline-design/SKILL.md", + "old": "description: >", + "new": "description: >\n Also use for output aggregation, collectFile headers, join cardinality,\n grouping keys and null-handling correctness." + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "description: Launch Nextflow pipeline executions on cloud and HPC clusters via Nextflow Platform. Use when the user wants to run/launch/submit a pipeline on a cloud or cluster compute environment, configure a compute environment, push pipeline changes to GitHub before launching, or sign in to Nextflow Platform.", + "new": "description: >\n Plan, launch or resume Nextflow pipelines locally or through Nextflow Platform.\n Use for pre-launch questions about uncommitted/unpublished changes, revision\n selection, parameters, compute resources and resume identity, as well as\n submission and readback. Publication and infrastructure creation require\n separate explicit authorization; a launch question does not authorize them." + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "# Launch Pipeline on Nextflow Platform", + "new": "# Launch or Resume a Pipeline\n\n## Local runs and resume\n\nFor a local run, confirm the user's pipeline, parameters, executor and output destination. Use the installed release's `nextflow run` interface; a local run does not require Platform authentication, a remote Git repository or Nextflow 26.04.\n\nBefore resuming, read [run identification](../debug-local-run/references/run-identification.md) and verify the requested run/session and accessible work/cache metadata. Use `-resume` with the selected identity; do not choose a run solely because it is newest. Inspect completion status and representative outputs; a cache hit alone is not scientific-output verification.\n\nFor missing runtime setup, read [runtime setup](../build-nextflow-pipeline/references/install-nextflow/README.md). Stop before installing or upgrading without explicit approval.\n\n## Platform launches" + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "3. **Upload local changes** — push any uncommitted local changes to the remote so the launched run reflects the user's current code.", + "new": "3. **Select a published revision** — verify that the remote contains the intended code. Publishing local changes requires separate explicit approval; a launch request alone is not authority to commit or push." + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "Initialize Git if needed, review the user's selected pipeline files, and stage\nonly the intended changes. Help the user create or select a remote repository,\nconfigure its remote URL, and push the agreed revision using the available tools.", + "new": "Explain the missing published revision and ask for separate authorization before initializing Git, creating a remote, staging files or publishing code. Alternatively select an already published revision the user approves." + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "Before launching, push any local changes so the remote reflects the code that should run:\n\nReview the changes, commit the user's intended pipeline files with a descriptive\nmessage, and push the confirmed branch using the available Git tools.", + "new": "Compare local changes with the selected remote revision. If the intended code is unpublished, stop and ask whether the user wants a separate commit/push task or a launch of the existing published revision. Only publish after explicit approval, staging only the approved files." + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "4. **PUSH local changes first** — the launched run uses the remote code, so local edits must be committed and pushed.", + "new": "4. **VERIFY the published revision** — use the approved remote code; obtain separate authorization before committing or pushing local changes." + }, + { + "path": "skills/launch-workflow/SKILL.md", + "old": "`nextflow launch` returns a run URL on Nextflow Platform. Present this URL to the user so they can monitor progress in the Platform UI.", + "new": "`nextflow launch` returns a run URL on Nextflow Platform. Retrieve the authoritative submitted workflow using discovered MCP operations and confirm its revision, parameters, compute environment and resume identity. Present the verified run identifier/URL and distinguish submission from successful completion." + } + ] + }, + { + "folds": [ + { + "from": "nf-plugin-legacy-migration", + "to": "nf-plugin-development", + "label": "legacy plugin migration", + "heading": "Legacy plugin migration", + "when": "When migrating an existing legacy plugin, preserve extension behavior and validate the target registry and Nextflow release; publishing needs explicit authorization." + } + ] + } + ] +} diff --git a/tools/curation/nf-core-safety.md b/tools/curation/nf-core-safety.md new file mode 100644 index 0000000..58a7274 --- /dev/null +++ b/tools/curation/nf-core-safety.md @@ -0,0 +1,9 @@ +# nf-core safety in the core plugin + +When a project declares nf-core conventions, preserve its scaffolding, schema, samplesheet checks, software-version emissions and resource profiles. Match publication syntax to the project's supported Nextflow release and existing output contract; legacy examples do not mandate replacing workflow outputs with publishDir. + +Inspect the repository's contribution rules and actual branches before editing. nf-core commonly develops on dev and releases from main/master; verify this repository rather than unconditionally switching branches. Opening or merging PRs requires the user's authorization. + +Shared modules are upstream-owned: avoid silently modifying them in place. Prefer a documented local adapter or approved upstream change; preserve the shared module's input/output contract and dependency pins. Run the applicable installed nf-core lint checks and representative tests before claiming compliance. + +Template synchronization, bulk module updates and upstream contributions are separate maintenance work. If explicitly requested, use `nextflow-nf-core:maintain-nf-core-pipeline` when that pack is enabled. Otherwise explain the missing pack and ask the user to install/enable it; do not silently install plugins or expand a conversion into maintenance. diff --git a/tools/curation/optional-packs.md b/tools/curation/optional-packs.md new file mode 100644 index 0000000..49b4af7 --- /dev/null +++ b/tools/curation/optional-packs.md @@ -0,0 +1,16 @@ +# Optional Nextflow packs + +Inspect the session's available skill inventory before invoking a specialist. If the namespaced skill is available, use it for the requested task. If not, explain which pack is needed and ask the user to explicitly install/enable it. Do not silently install plugins, invoke a missing skill or access paths outside the current plugin root. + +| Requested task | Optional skill | +| --- | --- | +| Create compute environments or credentials | `nextflow-platform:ce-credentials-setup` | +| Create/update storage data links | `nextflow-platform:seqera-data-links` | +| Write declarative Platform provisioning YAML | `nextflow-platform:seqerakit` | +| Run omics analysis or acquire GEO/SRA datasets | `nextflow-nf-core:nextflow-development` | +| Template sync or upstream nf-core maintenance | `nextflow-nf-core:maintain-nf-core-pipeline` | +| Develop or migrate a Nextflow extension plugin | `nextflow-plugins:nf-plugin-development` | +| Broad run/cache history or storage analysis | `nextflow-provenance:nextflow-history` | +| Trace lineage-store output origins | `nextflow-provenance:nf-data-lineage` | + +All packs share the enabled `nextflow` core plugin's hosted Seqera connection. They carry only discovery/safety guidance, not duplicate MCP servers or API schemas. Credential, infrastructure, publication and destructive changes need explicit authorization. Core debugging, run identification, ordinary launch/resume and basic nf-core-safe edits remain available without optional packs. diff --git a/tools/curation/run-identification.md b/tools/curation/run-identification.md new file mode 100644 index 0000000..c7d2328 --- /dev/null +++ b/tools/curation/run-identification.md @@ -0,0 +1,9 @@ +# Identify the selected local run before debugging or resuming + +Read history in the environment that owns the run, using the installed release's command help and user-selected workspace. `nextflow log` lists runs; `nextflow log ` retrieves selected task metadata. Record the run name/session ID, pipeline revision, command/parameters, status and work directory before choosing a resume target. + +Confirm that the selected work directory and cache metadata are accessible. A newer run, matching filename or cache hit does not prove that it is the intended analysis. Inspect the selected task's .command files and outputs when diagnosing failures; distinguish cached reuse, submission and completed output verification. + +Read-only inspection does not authorize cleanup, deletion, installation or rerunning a pipeline. Ask for approval before mutations; `nextflow clean` can destroy work required for resume. + +Broad historical recaps and storage analysis belong to `nextflow-provenance:nextflow-history`; output-origin/LID exploration belongs to `nextflow-provenance:nf-data-lineage`. Use those skills only when the optional pack is enabled; ordinary debugging and resume selection do not require it. diff --git a/tools/import_package.py b/tools/import_package.py index 33abbb0..8d0ec21 100644 --- a/tools/import_package.py +++ b/tools/import_package.py @@ -36,7 +36,7 @@ # Version of the Claude plugin. It is released independently of the generic package # because the Claude build curates the skill set below; bump it on every release. -VERSION = "0.2.2" +VERSION = "0.3.0" # Skills from the generic package that are not shipped in the Claude plugin. EXCLUDED_SKILLS = [ @@ -209,6 +209,9 @@ def main() -> None: else: shutil.copy2(src, dst) + # Optional output is generated, never copied from the upstream package. + if (REPO / "packs").exists(): + shutil.rmtree(REPO / "packs") relicense_portal_files() curate_skills() subprocess.run([ @@ -283,6 +286,11 @@ def main() -> None: if not (REPO / ICON).is_file(): sys.exit(f"icon not found: {ICON}") + subprocess.run([ + sys.executable, "-I", str(REPO / "tools" / "build_skill_packs.py"), + "--root", str(REPO), + ], check=True) + skills = sorted(p.parent.name for p in (REPO / "skills").glob("*/SKILL.md")) print(f"imported {name} {version}: {len(skills)} skills") diff --git a/tools/skill_packs.json b/tools/skill_packs.json new file mode 100644 index 0000000..14d93ed --- /dev/null +++ b/tools/skill_packs.json @@ -0,0 +1,81 @@ +{ + "core": [ + "build-nextflow-pipeline", + "nf-pipeline-design", + "repair-workflow", + "debug-local-run", + "debug-seqera-failed-run", + "nf-test", + "migrate-nextflow-code", + "nextflow-schema", + "nextflow-config", + "create-container", + "launch-workflow" + ], + "consolidations": "core_skill_consolidations.json", + "packs": [ + { + "name": "nextflow-platform", + "description": "Optional Nextflow Platform compute/credential setup, storage data links and seqerakit automation. Requires the enabled nextflow core plugin.", + "skills": [ + "ce-credentials-setup", + "seqera-data-links", + "seqerakit" + ] + }, + { + "name": "nextflow-nf-core", + "description": "Optional nf-core analysis, GEO/SRA acquisition, template synchronization and pipeline maintenance. Requires the enabled nextflow core plugin.", + "skills": [ + "nextflow-development", + "maintain-nf-core-pipeline" + ] + }, + { + "name": "nextflow-plugins", + "description": "Optional Nextflow plugin development and legacy registry migration. Requires the enabled nextflow core plugin.", + "skills": [ + "nf-plugin-development" + ] + }, + { + "name": "nextflow-provenance", + "description": "Optional run/cache history analysis and lineage-store exploration. Requires the enabled nextflow core plugin.", + "skills": [ + "nextflow-history", + "nf-data-lineage" + ] + } + ], + "resources": [ + { + "path": "skills/build-nextflow-pipeline/references/nf-core-safety.md", + "source": "curation/nf-core-safety.md" + }, + { + "path": "skills/debug-local-run/references/run-identification.md", + "source": "curation/run-identification.md" + }, + { + "path": "skills/build-nextflow-pipeline/references/optional-packs.md", + "source": "curation/optional-packs.md" + }, + { + "path": "packs/nextflow-platform/references/mcp-connection.md", + "source": "curation/mcp-connection.md" + }, + { + "path": "packs/nextflow-nf-core/references/mcp-connection.md", + "source": "curation/mcp-connection.md" + }, + { + "path": "packs/nextflow-plugins/references/mcp-connection.md", + "source": "curation/mcp-connection.md" + }, + { + "path": "packs/nextflow-provenance/references/mcp-connection.md", + "source": "curation/mcp-connection.md" + } + ], + "core_guidance": true +} diff --git a/tools/test_consolidate_skills.py b/tools/test_consolidate_skills.py index 30c98c8..93cc3ba 100644 --- a/tools/test_consolidate_skills.py +++ b/tools/test_consolidate_skills.py @@ -99,6 +99,15 @@ def test_behavioral_edit_is_applied_and_replayable(self): self.assertEqual(self.run_cli().returncode, 0) self.assertEqual((self.root / "sources.json").read_bytes(), before) + def test_a_second_plan_keeps_the_previous_consolidation_record(self): + path = self.root / "sources.json" + sources = json.loads(path.read_text()) + sources["claude_curation"]["consolidated_skills"] = [{"from": "previous", "to": "caller"}] + path.write_text(json.dumps(sources)) + self.assertEqual(self.run_cli().returncode, 0) + recorded = json.loads(path.read_text())["claude_curation"]["consolidated_skills"] + self.assertEqual(recorded, [{"from": "previous", "to": "caller"}, {"from": "old", "to": "owner"}]) + def test_missing_source_and_guide_fails_explicitly(self): import shutil shutil.rmtree(self.root / "skills/old") diff --git a/tools/test_skill_packs.py b/tools/test_skill_packs.py new file mode 100644 index 0000000..a227d95 --- /dev/null +++ b/tools/test_skill_packs.py @@ -0,0 +1,144 @@ +"""Test generated plugin boundaries through the public pack-builder CLI.""" + +import hashlib +import json +import subprocess +import sys +import tempfile +import unittest +from pathlib import Path + +CLI = Path(__file__).with_name("build_skill_packs.py") + + +class SkillPackTests(unittest.TestCase): + def setUp(self): + self.tmp = tempfile.TemporaryDirectory() + self.addCleanup(self.tmp.cleanup) + self.root = Path(self.tmp.name) + files = { + "skills/owner/SKILL.md": "---\nname: owner\ndescription: Build workflows\n---\n# Build\nUse `history`. Read [history](../history/SKILL.md).\n", + "skills/history/SKILL.md": "---\nname: history\ndescription: Explain history\n---\n# History\nRead [owner](../owner/SKILL.md) and [details](references/details.md).\n", + "skills/history/references/details.md": "Preserve cache semantics.\n", + "skills/history/scripts/check.sh": "#!/bin/sh\nprintf 'history checked\\n'\n", + } + entries = [] + for relative, content in files.items(): + path = self.root / relative + path.parent.mkdir(parents=True, exist_ok=True) + path.write_text(content) + digest = hashlib.sha256(content.encode()).hexdigest() + entries.append({"path": relative, "source": "upstream/" + relative, + "source_sha256": digest, "bundled_sha256": digest}) + (self.root / "sources.json").write_text(json.dumps({"files": entries, "claude_curation": {"edited_files": []}})) + manifest = self.root / ".claude-plugin/plugin.json" + manifest.parent.mkdir() + manifest.write_text(json.dumps({"name": "nextflow", "version": "0.3.0", "description": "Pipeline authoring"})) + (self.root / ".claude-plugin/marketplace.json").write_text(json.dumps({"name": "nextflow-claude-plugin", "owner": {"name": "Seqera"}, "plugins": [{"name": "nextflow", "source": "./", "version": "0.3.0"}]})) + (self.root / ".mcp.json").write_text('{"mcpServers": {"seqera": {"type": "http", "url": "https://mcp.seqera.io/mcp"}}}') + self.plan = self.root / "packs.json" + self.plan.write_text(json.dumps({"core": ["owner"], "packs": [{"name": "nextflow-provenance", "description": "History", "skills": ["history"]}], "resources": []})) + + def run_cli(self): + return subprocess.run([sys.executable, "-I", str(CLI), "--root", str(self.root), "--plan", str(self.plan)], text=True, capture_output=True) + + def test_moves_complete_skill_and_preserves_original_provenance(self): + result = self.run_cli() + self.assertEqual(result.returncode, 0, result.stderr) + self.assertEqual({p.name for p in (self.root / "skills").iterdir()}, {"owner"}) + pack = self.root / "packs/nextflow-provenance" + self.assertEqual((pack / "skills/history/references/details.md").read_text(), "Preserve cache semantics.\n") + self.assertEqual((pack / "skills/history/scripts/check.sh").read_text(), "#!/bin/sh\nprintf 'history checked\\n'\n") + self.assertIn("[details](references/details.md)", (pack / "skills/history/SKILL.md").read_text()) + self.assertIn("`nextflow:owner`", (pack / "skills/history/SKILL.md").read_text()) + self.assertNotIn("../owner/SKILL.md", (pack / "skills/history/SKILL.md").read_text()) + self.assertIn("`nextflow-provenance:history`", (self.root / "skills/owner/SKILL.md").read_text()) + manifest = json.loads((pack / ".claude-plugin/plugin.json").read_text()) + self.assertNotIn("dependencies", manifest) # Installing a pack must not silently install core. + self.assertFalse((pack / ".mcp.json").exists()) + sources = json.loads((self.root / "sources.json").read_text()) + moved = next(e for e in sources["files"] if e["path"].endswith("history/references/details.md")) + self.assertEqual(moved["source"], "upstream/skills/history/references/details.md") + for entry in sources["files"]: + self.assertEqual(entry["bundled_sha256"], hashlib.sha256((self.root / entry["path"]).read_bytes()).hexdigest()) + local_sources = json.loads((pack / "sources.json").read_text()) + self.assertIn("skills/history/references/details.md", {e["path"] for e in local_sources["files"]}) + for entry in local_sources["files"]: + self.assertEqual(entry["bundled_sha256"], hashlib.sha256((pack / entry["path"]).read_bytes()).hexdigest()) + marketplace = json.loads((self.root / ".claude-plugin/marketplace.json").read_text()) + self.assertEqual([(p["name"], p["source"]) for p in marketplace["plugins"]], [("nextflow", "./"), ("nextflow-provenance", "./packs/nextflow-provenance")]) + + def test_completed_generation_is_byte_identical_on_replay(self): + self.assertEqual(self.run_cli().returncode, 0) + before = {str(p.relative_to(self.root)): p.read_bytes() for p in self.root.rglob("*") if p.is_file()} + self.assertEqual(self.run_cli().returncode, 0) + after = {str(p.relative_to(self.root)): p.read_bytes() for p in self.root.rglob("*") if p.is_file()} + self.assertEqual(after, before) + + def test_unknown_inventory_fails_before_moving_anything(self): + rogue = self.root / "skills/unclassified/SKILL.md" + rogue.parent.mkdir() + rogue.write_text("unexpected upstream skill") + result = self.run_cli() + self.assertNotEqual(result.returncode, 0) + self.assertIn("skill pack inventory mismatch", result.stderr) + self.assertTrue((self.root / "skills/history/SKILL.md").is_file()) + self.assertFalse((self.root / "packs").exists()) + + def test_missing_generated_resource_is_not_an_idempotent_success(self): + self.assertEqual(self.run_cli().returncode, 0) + (self.root / "packs/nextflow-provenance/skills/history/references/details.md").unlink() + result = self.run_cli() + self.assertNotEqual(result.returncode, 0) + self.assertIn("missing bundled file", result.stderr) + + def test_unrecorded_imported_asset_is_kept_with_an_explicit_origin_gap(self): + asset = self.root / "skills/history/requirements.txt" + asset.write_text("pyyaml\n") + self.assertEqual(self.run_cli().returncode, 0) + sources = json.loads((self.root / "sources.json").read_text()) + entry = next(e for e in sources["files"] if e["path"].endswith("requirements.txt")) + self.assertEqual(entry["source_sha256"], hashlib.sha256(b"pyyaml\n").hexdigest()) + self.assertIn("No upstream provenance entry", entry["note"]) + self.assertEqual((self.root / entry["path"]).read_text(), "pyyaml\n") + + def check_cli(self): + return subprocess.run([sys.executable, "-I", str(CLI.with_name("check_sources.py")), "--root", str(self.root)], text=True, capture_output=True) + + def test_checker_rejects_a_link_that_only_works_in_the_monorepo(self): + self.assertEqual(self.run_cli().returncode, 0) + path = self.root / "packs/nextflow-provenance/skills/history/SKILL.md" + path.write_text(path.read_text() + "\n[unsafe](../../../../skills/owner/SKILL.md)\n") + result = self.check_cli() + self.assertNotEqual(result.returncode, 0) + self.assertIn("link escapes installed plugin", result.stderr) + + def test_checker_rejects_a_duplicate_server_in_an_optional_pack(self): + self.assertEqual(self.run_cli().returncode, 0) + path = self.root / "packs/nextflow-provenance/.mcp.json" + path.write_text('{"mcpServers": {"seqera": {}}}') + result = self.check_cli() + self.assertNotEqual(result.returncode, 0) + self.assertIn("duplicate MCP connection", result.stderr) + + def test_checker_rejects_a_manifest_version_mismatch(self): + self.assertEqual(self.run_cli().returncode, 0) + path = self.root / "packs/nextflow-provenance/.claude-plugin/plugin.json" + manifest = json.loads(path.read_text()) + manifest["version"] = "99.0.0" + path.write_text(json.dumps(manifest)) + result = self.check_cli() + self.assertNotEqual(result.returncode, 0) + self.assertIn("name/version mismatch", result.stderr) + + def test_duplicate_assignment_is_rejected(self): + plan = json.loads(self.plan.read_text()) + plan["packs"][0]["skills"].append("owner") + self.plan.write_text(json.dumps(plan)) + result = self.run_cli() + self.assertNotEqual(result.returncode, 0) + self.assertIn("assigned more than once", result.stderr) + + +if __name__ == "__main__": + unittest.main() diff --git a/tools/verify_conversion_fixture.py b/tools/verify_conversion_fixture.py new file mode 100644 index 0000000..8f9db1c --- /dev/null +++ b/tools/verify_conversion_fixture.py @@ -0,0 +1,83 @@ +#!/usr/bin/env python3 +"""Execute an inspected, model-produced synthetic conversion against golden vectors. + +This is a local smoke check, not a general scientific-equivalence evaluation. +The workspace must contain the authored eval fixture plus its generated main.nf. +""" + +import argparse +import csv +import json +import os +import shutil +import subprocess +import tempfile +from pathlib import Path + +KNOWN_INPUT = "id\tvalue\na\t3\nb\t5\n" +KNOWN_OUTPUT = "id\tscore\na\t8\nb\t24\n" +HOLDOUT_INPUT = "id\tvalue\nc\t2\nd\t7\n" +HOLDOUT_OUTPUT = "id\tscore\nc\t3\nd\t48\n" + + +def verify_conversion_workspace(workspace: Path, nextflow: str = "nextflow") -> dict: + for command in ["snakemake", nextflow]: + if not shutil.which(command): + raise ValueError(f"missing fixture runtime: {command}; no installation was attempted") + for filename in ["Snakefile", "transform.py", "main.nf", "nextflow.config"]: + if not (workspace / filename).is_file(): + raise ValueError(f"missing conversion fixture: {filename}") + with tempfile.TemporaryDirectory(prefix="nextflow-conversion-proof-") as tmp: + root = Path(tmp) + project = root / "project" + shutil.copytree(workspace, project) + home = root / "home" + home.mkdir() + env = {**os.environ, "HOME": str(home), "NXF_HOME": str(root / "nxf-home"), "NXF_ANSI_LOG": "false", "NXF_AGENT_MODE": "false"} + commands = [] + + def run(*args): + result = subprocess.run(args, cwd=project, env=env, text=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=180) + commands.append({"command": list(args), "exit_code": result.returncode, "output": result.stdout}) + if result.returncode: + raise ValueError(f"fixture command failed: {' '.join(args)}\n{result.stdout}") + return result.stdout + + (project / "input.tsv").write_text(KNOWN_INPUT) + (project / "baseline.tsv").unlink(missing_ok=True) + run("snakemake", "--cores", "1", "baseline.tsv") + if (project / "baseline.tsv").read_text() != KNOWN_OUTPUT: + raise ValueError("source workflow disagrees with independent known-output oracle") + for label, inputs, expected in [("known", KNOWN_INPUT, KNOWN_OUTPUT), ("holdout", HOLDOUT_INPUT, HOLDOUT_OUTPUT)]: + (project / "input.tsv").write_text(inputs) + outdir = project / f"outputs-{label}" + run(nextflow, "-C", "nextflow.config", "run", "main.nf", "-name", f"fixture-{label}", "--input", "input.tsv", "--outdir", str(outdir), "-work-dir", str(project / "work"), "-with-trace", f"trace-{label}.tsv") + actual = outdir / "result.tsv" + if not actual.is_file() or actual.read_text() != expected: + raise ValueError(f"converted workflow disagrees with independent {label} oracle") + run(nextflow, "-C", "nextflow.config", "run", "main.nf", "-name", "fixture-resume", "--input", "input.tsv", "--outdir", str(project / "outputs-holdout"), "-work-dir", str(project / "work"), "-resume", "fixture-holdout", "-with-trace", "trace-resume.tsv") + with (project / "trace-resume.tsv").open() as trace: + tasks = list(csv.DictReader(trace, delimiter="\t")) + if not tasks or any(task["status"] != "CACHED" for task in tasks): + raise ValueError("selected run did not resume cached tasks") + if (project / "outputs-holdout/result.tsv").read_text() != HOLDOUT_OUTPUT: + raise ValueError("resume changed the verified output") + version = run(nextflow, "-version").strip() + return {"status": "pass", "nextflow_version": version, "workspace": str(workspace), "known_output": KNOWN_OUTPUT, "holdout_output": HOLDOUT_OUTPUT, "resume_statuses": [task["status"] for task in tasks], "commands": commands} + + +def main() -> None: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("workspace", type=Path, help="inspected native-eval workspace") + parser.add_argument("--report", type=Path) + parser.add_argument("--nextflow", default="nextflow", help="explicitly selected installed runtime; no installation or upgrade") + args = parser.parse_args() + report = verify_conversion_workspace(args.workspace.resolve(), args.nextflow) + if args.report: + args.report.parent.mkdir(parents=True, exist_ok=True) + args.report.write_text(json.dumps(report, indent=2) + "\n") + print("PASS source execution, known/holdout output comparisons and named cached resume") + + +if __name__ == "__main__": + main() diff --git a/tools/verify_skill_packs.py b/tools/verify_skill_packs.py new file mode 100644 index 0000000..1e63fb8 --- /dev/null +++ b/tools/verify_skill_packs.py @@ -0,0 +1,80 @@ +#!/usr/bin/env python3 +"""Verify actual Claude discovery in fresh configs, without credentials or API calls.""" + +import argparse +import json +import os +import re +import subprocess +import tempfile +from pathlib import Path + +REPO = Path(__file__).resolve().parent.parent +EXPECTED = { + "nextflow": {"build-nextflow-pipeline", "nf-pipeline-design", "repair-workflow", "debug-local-run", "debug-seqera-failed-run", "nf-test", "migrate-nextflow-code", "nextflow-schema", "nextflow-config", "create-container", "launch-workflow"}, + "nextflow-platform": {"ce-credentials-setup", "seqera-data-links", "seqerakit"}, + "nextflow-nf-core": {"nextflow-development", "maintain-nf-core-pipeline"}, + "nextflow-plugins": {"nf-plugin-development"}, + "nextflow-provenance": {"nextflow-history", "nf-data-lineage"}, +} + + +def verify_claude_installations(root: Path) -> dict: + scenarios = [["nextflow"]] + [["nextflow", name] for name in EXPECTED if name != "nextflow"] + scenarios += [list(EXPECTED), ["nextflow-plugins"]] + report = {"claude_version": subprocess.check_output(["claude", "--version"], text=True).strip(), "scenarios": []} + for names in scenarios: + with tempfile.TemporaryDirectory(prefix="nextflow-pack-install-") as config: + env = {**os.environ, "CLAUDE_CONFIG_DIR": config} + + def command(*args): + result = subprocess.run(["claude", "plugin", *args], cwd=root, env=env, text=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, timeout=90) + if result.returncode: + raise ValueError(f"Claude plugin command failed ({' '.join(args)}):\n{result.stdout}") + return result.stdout + + command("marketplace", "add", str(root)) + for name in names: + command("install", f"{name}@nextflow-claude-plugin") + installed = command("list") + total_skills = 0 + total_servers = 0 + inventories = {} + for name in names: + details = command("details", f"{name}@nextflow-claude-plugin") + match = re.search(r"Skills \((\d+)\)\s+([^\n]+)", details) + if not match: + raise ValueError(f"Claude did not report skills for {name}: {details}") + actual = set(match.group(2).strip().split(", ")) + if actual != EXPECTED[name] or int(match.group(1)) != len(actual): + raise ValueError(f"Claude skill discovery mismatch for {name}: {sorted(actual)}") + servers = re.search(r"MCP servers \((\d+)\)", details) + if not servers: + raise ValueError(f"Claude did not report MCP inventory for {name}") + count = int(servers.group(1)) + if count != (1 if name == "nextflow" else 0): + raise ValueError(f"Unexpected MCP registrations for {name}: {count}") + total_skills += len(actual) + total_servers += count + inventories[name] = sorted(actual) + for name in EXPECTED: + if name not in names and f"{name}@nextflow-claude-plugin" in installed: + raise ValueError(f"Plugin silently installed: {name}") + report["scenarios"].append({"plugins": names, "skills": total_skills, "mcp_servers": total_servers, "inventories": inventories, "status": "pass"}) + print(f"PASS {' + '.join(names)}: {total_skills} skills, {total_servers} MCP servers") + return report + + +def main() -> None: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--root", type=Path, default=REPO) + parser.add_argument("--report", type=Path) + args = parser.parse_args() + report = verify_claude_installations(args.root.resolve()) + if args.report: + args.report.parent.mkdir(parents=True, exist_ok=True) + args.report.write_text(json.dumps(report, indent=2) + "\n") + + +if __name__ == "__main__": + main() diff --git a/verification/11-skill-core.md b/verification/11-skill-core.md new file mode 100644 index 0000000..41f5c06 --- /dev/null +++ b/verification/11-skill-core.md @@ -0,0 +1,85 @@ +# Eleven-skill core verification + +Scope: follow-up to PR #1's 28-skill catalog (`cfa99eb`). Implementation: `1fac28b`, with the behavioral suite and execution harness committed separately. No release/tag, production change or authenticated Platform operation was performed. + +## Packaging and discovery + +- **17 CLI tests passed:** eight consolidation tests and nine pack-generation/boundary tests. +- **147 bundled file records verified:** hashes, original provenance, complete skill resources, per-pack provenance manifests and local links within installed plugin roots. +- Marketplace and all five plugin manifests pass strict Claude validation. +- Full importer replay from a synthetic generic package reproduces core, packs and provenance; repeated imports are identical. The fixture reverses public curation and supplies placeholders for excluded entrypoints, not a private upstream package. + +Actual isolated installation results, using Claude Code **2.1.293**: + +| Enabled plugins | Discovered skills | Registered MCP servers | +| --- | ---: | ---: | +| Core | 11 | 1 | +| Core + platform | 14 | 1 | +| Core + nf-core | 13 | 1 | +| Core + plugins | 12 | 1 | +| Core + provenance | 13 | 1 | +| Core + all four packs | 19 | 1 | +| Plugins pack alone | 1 | 0 | + +Exact skill names, not just counts, were checked. No unrequested plugin was installed. These are connection-registration checks; they do not establish OAuth authentication or live API behavior. CI repeats the matrix with its pinned Claude version. + +One pre-existing `requirements.txt` lacked an upstream provenance entry. It is retained with an explicit origin-gap note and a hash of the imported bytes; no canonical upstream identity was invented. Repackaged license files normalize only trailing newlines, retain their original source hash, and record a bundled override when needed. + +## Behavioral smoke tests + +Nine cases passed across **three runs each (27/27)** using Sonnet and Haiku graders: + +1. Read-only conversion readiness: missing helper/data references and honest access uncertainty. +2. Native single-module advice without a wrapper or invented inputs. +3. Single-tool construction without mandatory alternative branches; baseline comparisons remain required. +4. Header/aggregation correctness rather than relying on successful execution. +5. Script placement/staging without forcing an image build. +6. Missing platform pack: explicit named installation help and a safe stop. +7. Pre-launch publication authority: a launch question does not authorize commit/push. +8. Small Snakemake conversion: runnable output and honest unexecuted verification handoff. +9. Installed optional plugin specialist: legacy registry migration assessment through its preserved playbook. + +The first suite exposed missing-pack naming and pre-launch discovery gaps; core descriptions were corrected. A trivial conversion can be solved without invoking Skill, so its hard checks are produced artifacts, verification honesty and subsequent real execution. Other cases retain explicit skill-discovery checks. + +Bash-enabled native evaluation was refused by Claude's SSH-store symlink security check. It was not bypassed or weakened. The successful suite grants Read/Glob/Grep/Skill/Write/Edit only, runs authored synthetic scaffolds, starts no real MCP servers, and keeps reports local. + +## Real execution/output evidence + +Three separately generated, inspected conversions were materialized from public Write-tool trace payloads; sealed eval directories were not unsealed. Each was executed in a fresh temporary project: + +- Run the source Snakefile with Snakemake **9.19.0**. +- Compare source and converted outputs against independently specified values: inputs 3 and 5 produce 8 and 24. +- Execute a holdout input: 2 and 7 produce 3 and 48. +- Confirm helper staging and publication to the selected output directory. +- Resume the explicitly selected `fixture-holdout` run; task trace reports **CACHED**, and the output remains correct. + +All three conversions passed. The executable's own version report identifies **Nextflow 26.04.4**, regardless of the Homebrew launcher's directory label. The harness records the actual runtime and uses `-C` with the fixture config to avoid unrelated user configuration. No user runtime installation or upgrade was performed. + +The installed 26.06-edge launcher failed before executing the fixture because it tried to download unavailable `nf-seqera@1.0.0`. Disabling agent mode and isolating config did not fix that launcher's startup. Execution results therefore establish this synthetic contract on **26.04.4**, not execution compatibility with that edge runtime. + +## Limits + +- No general scientific-equivalence or optimal-catalog-size claim: this is one small deterministic conversion fixture plus bounded routing tests. +- No registry module was actually executed; its case checks release-aware native advice and scope boundaries. +- No production launch, cloud provisioning, credential change, template merge, registry publication or lineage-store mutation was attempted. +- MCP Skills-extension support, Portal host behavior and the private generic package remain outside this PR's verified scope. + +## Reproduce + +```bash +python3 -I tools/test_consolidate_skills.py +python3 -I tools/test_skill_packs.py +python3 -I tools/check_sources.py +python3 -I tools/verify_skill_packs.py --report /tmp/pack-installations.json +claude plugin eval . --trust-plugin --no-publish --ablation none \ + --runs 3 --allow-tools Write Edit --scaffold --keep-temp +``` + +After inspecting/materializing a conversion's synthetic workspace, select an installed executable and verify its reported release: + +```bash +python3 -I tools/verify_conversion_fixture.py /path/to/inspected-fixture \ + --nextflow /path/to/installed-nextflow --report /tmp/conversion-proof.json +``` + +Model smoke tests consume the operator's Claude quota; they are not run by unauthenticated CI. Temporary execution projects are removed by the harness. Raw machine-local model traces, reports and account data are not included in this repository.