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Merged
kopardev merged 5 commits into from
Sep 25, 2026
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docs(motif): clarify motif enrichment outputs and interpretation #146

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bde9de5
Merge branch 'main' of github.com:CCBR/ASPEN
kopardev Sep 17, 2026
78a01ea
Merge branch 'main' of github.com:CCBR/ASPEN
kopardev Sep 21, 2026
3d14028
docs(motif): clarify motif enrichment outputs
kopardev Sep 24, 2026
1c9ce03
docs(changelog): record motif docs update
kopardev Sep 24, 2026
4bb0d11
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 24, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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## ASPEN development version

- Clarify motif enrichment outputs and interpretation in the documentation: fix the reported location of HOMER/AME result folders, explain how ASPEN reuses HOMER-generated `target.fa`/`background.fa` in AME, document the AME parallelization strategy, and add simpler guidance for interpreting `knownResults.txt` and `ame_results.txt`. (#146, @kopardev)

## ASPEN 1.4.0

- Add structured pipeline state tracking: a `pipeline.status.json` sidecar and `pipeline.{running,completed,failed,canceled}` marker files are now written to `WORKDIR` during `run`, with a live progress monitor that periodically updates `pipeline.running` with a step-completion percentage; a best-effort `jobby` TSV summary (`snakemake.log.jobby`) is now also generated when Slurm submission fails before Snakemake starts. Consolidated shared logging/banner/version-tag helper functions into a new staged library (`workflow/scripts/ccbr_pipeline_logging.sh`, slated for future migration to `ccbr_tools`); redesigned the `--version`/banner output. (#119, @kopardev)
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