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Include the failing Snakemake rule and command in pipeline.status.json and pipeline.failed so failed runs point directly to the offending step.\n\n⚡ Generated using AI ⚡
Skip the "Submit run with..." NEXT hint after a dry-run that reports "Nothing to be done", since there is no pending work to submit. ⚡ Generated using AI ⚡
…to rule all
deeptools_prep/deeptools_mat outputs were never requested by rule all
(or any other rule), so Snakemake never scheduled them regardless of
config/container fixes -- dry-run always reported "Nothing to be done"
even when the .mat.gz files had never been created.
- Add deeptools_plot rule: runs plotHeatmap/plotProfile on the TSS and
metagene matrices to produce the final, user-facing heatmap/profile
PDFs (results/deeptools/{group}.{bamtype}.{TSS,metagene}.{heatmap,profile}.pdf).
- Wire the new PDF outputs into rule all so they're actually scheduled.
- Fix deeptools_mat to use the workdir's configured genome's TSS BED
archive (config[GENOME]["tssBed"]) instead of an always-hardcoded
hg38_tssbeds.tar.gz, since ASPEN supports multiple genomes.
- Drop the unused {bedtype} wildcard from deeptools_mat/deeptools_plot;
it was never populated by any config/rule and unused in the shell
logic.
- Add a deeptools_plot entry to resources/cluster.json.
- Update docs/outputs.md to describe the actual output filenames and
location instead of the previously documented, never-implemented
protein_coding/all_samples naming scheme.
Validated with a real dry-run against a live workdir: previously
reported "Nothing to be done", now correctly schedules deeptools_prep,
deeptools_mat, and deeptools_plot jobs.
⚡ Generated using AI ⚡
for more information, see https://pre-commit.ci
Document when deepTools outputs are generated, how to interpret them, and which normalization and annotation defaults apply. Expand the documentation content area and keep table columns aligned on large displays. _commit message is ai-generated_ ⚡ Generated using AI ⚡
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Changes
This PR completes the deeptools visualization pipeline by:
Added
deeptools_plotrule (ASAP: Deeptools peaks #7): Generates the finalplotHeatmap/plotProfileTSS and metagene PDFs from thedeeptools_matmatrices. These outputs are now wired intorule allsodryrun/runactually schedule them. Previously, nothing requested these outputs so Snakemake silently never ran deepTools past matrix generation.Fixed
deeptools_matconfiguration: Now uses the workdir's configured genome's TSS BED archive (config[GENOME]["tssBed"]) instead of an always-hardcodedhg38_tssbeds.tar.gz. Removed the unused{bedtype}wildcard.Updated documentation (Document ASPEN dryrun/run console output examples #147):
docs/outputs.mdnow documents the actual output filenames and location (results/deeptools/{group}.{bamtype}.{TSS,metagene}.{heatmap,profile}.pdf) instead of the previously documented never-implementedprotein_coding/all_samplesnaming scheme.Improved diagnostics (#000): Failed-run diagnostics now record the failing Snakemake rule and command in
pipeline.status.jsonand the human-readablepipeline.failedmarker, so users can immediately see which step (e.g.,deeptools_mat) triggered the failure.Enhanced documentation (Document ASPEN dryrun/run console output examples #147): Added console output examples in
docs/deployment.mdwith screenshots, explainingSTEP/OK/INFO/NEXTmessages and explicit links between wrapper messages andWORKDIRstatus files.Minor improvements: Suppress the NEXT prompt in dryrun when nothing needs to be done, improving user experience.
Issues
Fixes #7 (primary feature - complete deeptools outputs and visualization)
Related to #147 (documentation)
Related to #152 (resource scaling - included in same branch)
Related to #148 (SLURM failure detection - included in same branch)
Related to #146 (motif enrichment docs - included in same branch)
PR Checklist
docs/outputs.md,docs/deployment.md, and added example console outputs)CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. (CHANGELOG.md updated with comprehensive entries)/data/Boufraqech_group/analysis/.temp/aspen_run_for_Ying_test5— exit code 0, all 13 steps completed, deeptools outputs verified)⚡ Generated using AI ⚡