Conversation
Add plans/ alongside existing plans_reviews/ for local, untracked planning docs (e.g. dedup vs filtered counts matrix plan, tracked in issue #138). ⚡ Generated using AI ⚡
Generate Tn5 nicking-site and read counts matrices, and the corresponding DiffATAC/DESeq2 results, from both dedup.bam (PCR/optical duplicates removed) and filtered.bam (duplicates retained, labeled nondedup), written to separate dedup/nondedup output subfolders. Previously only the duplicate-retaining filtered.bam was used. dedup is recommended for standard differential accessibility testing. Refs #138 ⚡ Generated using AI ⚡
Add an explicit check in _compute_downsampling_scaling_factors.py that exits with an actionable error message when a replicate has 0 reads aligned to the spike-in genome, instead of crashing with an opaque ZeroDivisionError. The compute_scaling_factors rule now also captures the script's stderr in a dedicated results/spikein/compute_scaling_factors.log so the message isn't buried in the main snakemake log. Fixes #139 ⚡ Generated using AI ⚡
Audit and fix documentation across docs/overview.md, docs/outputs.md, docs/introduction.md, docs/deployment.md, and docs/index.md: - Fix stale claims left over from the dedup/nondedup change. - Clarify how consensus peaks (pooled/consensus.bed/fixed-width ROI) and regions of interest are generated, with a why-two-rounds explanation and a table of which output to use for which downstream task. - Add ENCODE-referenced QC rule-of-thumb callouts for library complexity (NRF/PBC1/PBC2), TSS enrichment, and FRiP. - Consolidate scattered spike-in "when should I use this" guidance (previously split across overview.md and deployment.md) into a single decision-tree callout in overview.md, cross-linked from deployment.md. - Note that the embedded `aspen --help` output in deployment.md is an illustrative, point-in-time snapshot. - Remove the outdated, unreferenced docs/extra.md page; its content is superseded by docs/outputs.md. Update CHANGELOG.md with entries for this docs pass and the spike-in zero-reads fix. Refs #138, #139 ⚡ Generated using AI ⚡
The 1.3.0 heading was premature -- per repo convention the CHANGELOG heading stays as 'development version' while VERSION is a -dev suffix, and only gets renamed to the actual release version (e.g. 1.3.0) by the draft-release automation when preparing the release. ⚡ Generated using AI ⚡
for more information, see https://pre-commit.ci
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Changes
dedup.bam(PCR/optical duplicates removed) andfiltered.bam(duplicates retained, labelednondedup), written to separatededup/nondedupoutput subfolders.dedupis recommended for standard differential accessibility testing.ZeroDivisionErrorin_compute_downsampling_scaling_factors.py. The error is now also captured in a dedicatedresults/spikein/compute_scaling_factors.log.docs/overview.md,docs/outputs.md,docs/introduction.md,docs/deployment.md, anddocs/index.md:aspen --helpoutput indeployment.mdis an illustrative snapshot.docs/extra.mdpage.CHANGELOG.mdupdated with entries for all of the above under the development version heading.Issues
Closes #138
Fixes #139
PR Checklist
(
Strikethroughany points that are not applicable.)CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/Test run confirmed on biowulf (
/vf/users/Boufraqech_group/analysis/.temp/aspen_run_for_Ying_test2, 12 replicates,hs1_chrR, macs2 + genrich) at this PR's HEAD (58469c9). One replicate'salignjob hit the pre-existing24hwalltime limit incluster.jsonand was killed by SLURM; after bumping the walltime and resubmitting (--rerun-incomplete), the run completed successfully end-to-end (53 of 53remaining steps, exit code 0). The dedup/nondedup and spike-in fail-fast changes in this PR both worked as expected during validation. A separate reliability gap unrelated to this PR — Snakemake never detects SLURM jobs killed by timeout/OOM because ASPEN's cluster submission has no--cluster-statusscript — was filed as #141.⚡ Generated using AI ⚡