Add differential peak calling layer by dhusmann · Pull Request #3 · dhusmann/cutandrun

dhusmann · 2026-01-05T01:04:25Z

Summary

add differential peak calling subworkflow with DiffBind, ChIPBinner, SPAN diff + cross-comparison
add differential-only entrypoint and manifest writing for posthoc runs
add modules/scripts plus config/schema/docs/MultiQC updates and differential tests

Testing

pytest --keep-workflow-wd --tag test_differential (Slurm 12887126, COMPLETED 0:0)

dhusmann · 2026-01-05T01:04:32Z

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dhusmann · 2026-01-05T01:17:45Z

Resolved #3 (comment) by removing the gtf2bed dependency (parse GTF directly to TSS). Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12887984, COMPLETED 0:0).

dhusmann · 2026-01-05T01:17:55Z

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dhusmann · 2026-01-05T01:37:30Z

Resolved #3 (comment) by dropping runtime pip installs (hdbscan_grid uses numpy+hdbscan only and the process now uses an hdbscan container). Resolved #3 (comment) by emitting a combined chipbinner.significant.bed (up+down) and using it for cross-method overlaps. Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12888461, COMPLETED 0:0).

dhusmann · 2026-01-05T01:37:53Z

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dhusmann · 2026-01-05T01:49:31Z

Resolved #3 (comment) by guarding DiffBind results when FDR/log2FC columns are missing (empty significant set). Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12888753, COMPLETED 0:0).

dhusmann · 2026-01-05T01:49:44Z

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dhusmann · 2026-01-05T02:00:30Z

Resolved #3 (comment) by detecting whether the annotation BED includes a name column and only populating feature_id when present. Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12889044, COMPLETED 0:0).

dhusmann · 2026-01-05T02:00:47Z

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dhusmann · 2026-01-05T02:21:54Z

Resolved #3 (comment) by switching SPAN_COMPARE to a samtools container and using JAVA_CMD (if set) for OmniPeaks. Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12889436, COMPLETED 0:0).

dhusmann · 2026-01-05T02:22:12Z

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dhusmann · 2026-01-05T02:37:29Z

Resolved #3 (comment) by calling dba.report with th=1, fold=0 and applying filters downstream. Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12890114, COMPLETED 0:0).

dhusmann · 2026-01-05T02:37:49Z

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dhusmann · 2026-01-05T02:54:18Z

Resolved #3 (comment) by passing summary file paths directly into DIFFERENTIAL_SUMMARY_MERGE (no glob/overwrites). Retested: pytest --keep-workflow-wd --tag test_differential (Slurm 12890801, COMPLETED 0:0).

dhusmann · 2026-01-09T05:36:50Z

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dhusmann · 2026-01-09T05:50:25Z

Addressed pooled-control parsing in d3f1cdd:

Use known condition names from the manifest to derive condition/group (suffix match), with fallback to legacy split. Ref: Add differential peak calling layer #3 (comment)

dhusmann · 2026-01-09T05:50:48Z

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dhusmann · 2026-01-09T06:06:01Z

Addressed summary staging collision in ae4c3e5:

Stage summaries with a caller+group prefix (falls back safely) so diffbind callers don’t overwrite each other. Ref: Add differential peak calling layer #3 (comment)

dhusmann · 2026-01-09T06:06:27Z

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dhusmann · 2026-01-10T10:52:31Z

✅ Full pytest-workflow suite passed on Sherlock (Slurm).

Branch: differential_peak_calling
Commit: efbab9d

Most recent test-history entry (docs/test_history/differential_peak_calling.md):

2026-01-10 — differential tag + full pytest suite (Slurm)

Failure: ROTS error (rowSums(is.na(...)) expects matrix) when a condition has <2 replicates in test_differential_chipbinner (job 13175581, run dir /scratch/users/dhusmann/runs/pytest-suite/20260109_210345).
Fix: disable ROTS when <2 samples per condition and fall back to simple tests (or p=1 if <2) in bin/chipbinner_rots.R.
Failure: DIFFERENTIAL_SUMMARY_MERGE unbound variable due to $ in staged summary filename (job 13175959, run dir /scratch/users/dhusmann/runs/pytest-suite/20260109_212945).
Fix: stage summaries with stageAs: 'summaries/*' and build summary_files.list via find summaries -type f in modules/local/differential_summary.nf.
Failure: ANNOTATE_REGIONS container missing python (job 13177002, run dir /scratch/users/dhusmann/runs/pytest-suite/20260109_222413).
Fix: disable container for ANNOTATE_REGIONS so conda provides python (conf/modules.config).
Failure: ANNOTATE_REGIONS publishDir error (Unexpected path value from publishDir closure) (job 13178611, run dir /scratch/users/dhusmann/runs/pytest-suite/20260109_225233).
Fix: replace publishDir closure with a static map + enabled closure in modules/local/annotate_regions.nf.
Pass: test_differential_chipbinner tag rerun succeeded (job 13179209, run dir /scratch/users/dhusmann/runs/pytest-suite/20260109_231631).
Pass: full pytest suite succeeded (job 13179771, run dir /scratch/users/dhusmann/runs/pytest-suite/20260109_234549).

dhusmann · 2026-01-13T03:07:46Z

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dhusmann · 2026-01-14T02:42:36Z

Addressed #3 (comment) in commit a2d3e85: filter out NA FDR/log2FC rows before building significant beds so BED outputs never include NA coordinates.

dhusmann · 2026-01-14T02:42:58Z

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dhusmann · 2026-01-14T02:53:30Z

Addressed #3 (comment) in commit 6f3101c: explicitly label bins with missing cluster IDs as 'NA' so unassigned regions don't appear in stable beds.

dhusmann · 2026-01-14T02:53:49Z

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dhusmann · 2026-01-14T03:03:12Z

Addressed #3 (comment) in commit 0903658: keep an empty control map via ifEmpty([:]) so ChIPBinner still runs when no pooled controls exist.

dhusmann · 2026-01-14T03:03:31Z

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dhusmann · 2026-01-14T03:21:28Z

Addressed #3 (comment) in commit 1ef69b2: take the first capability result to make SPAN compare cmd/multibam settings a value channel so every group receives the same constants.

dhusmann · 2026-01-14T03:21:46Z

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dhusmann added 2 commits January 4, 2026 01:54

Add differential peak calling specifications

2aebdff

Add differential peak calling layer

f123e6e

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Comment thread bin/annotate_regions.py Outdated

Avoid gtf2bed dependency in annotate_regions

dcff1ff

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Comment thread modules/local/chipbinner_hdbscan_grid.nf Outdated

Comment thread subworkflows/local/differential_peak_calling.nf

Refine chipbinner clustering inputs

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Comment thread bin/diffbind_run.R

Handle empty DiffBind results

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Comment thread bin/annotate_regions.py

Handle unnamed annotation BEDs

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Comment thread modules/local/span_compare.nf Outdated

Ensure SPAN compare has samtools

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Comment thread bin/diffbind_run.R

Report full DiffBind results

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Comment thread modules/local/differential_summary.nf Outdated

Prevent summary file collisions

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Comment thread workflows/differential_only.nf Outdated

Use known conditions for pooled control parsing

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Comment thread modules/local/differential_summary.nf Outdated

Disambiguate differential summary staging

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Fix differential pytest failures and update history

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Comment thread bin/chipbinner_rots.R Outdated

Filter NA bins in chipbinner significant beds

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Comment thread bin/chipbinner_rots.R

Mark unassigned clusters as NA

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Comment thread subworkflows/local/differential_peak_calling.nf

Preserve empty control map for chipbinner

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Comment thread subworkflows/local/differential_peak_calling.nf

Broadcast SPAN capability values

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dhusmann commented Jan 5, 2026

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