Add differential peak calling extension by dhusmann · Pull Request #2 · dhusmann/cutandrun

dhusmann · 2026-01-04T13:53:52Z

Summary

add differential peak calling subworkflow with DiffBind, ChipBinner, and SPAN support plus summary/multiqc outputs
wire differential params into config/schema/docs and add differential-only workflow
add scripts/modules for manifest/design/annotation and new tests/assets

Testing

pytest --keep-workflow-wd tests/test_07_differential.yml

dhusmann · 2026-01-04T13:54:01Z

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dhusmann · 2026-01-04T14:18:04Z

Fix for #2 (comment)

Parse --diffbind_extra_params (JSON/YAML) and apply to DiffBind calls in bin/diffbind_run.R
Added conda deps for jsonlite/yaml

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12859643)

dhusmann · 2026-01-04T14:18:12Z

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cutandrun/workflows/cutandrun.nf

Lines 37 to 39 in d7bddb2

    
           // Check mandatory parameters that cannot be checked in the groovy lib as we want a channel for them 
        
           if (params.input) { ch_input = file(params.input) } else { exit 1, "Input samplesheet not specified!" }

Differential-only entrypoint still aborts for missing samplesheet

The new -entry DIFFERENTIAL_ONLY workflow is meant to consume precomputed manifests via --differential_from_run, but workflows/cutandrun.nf still executes at import time and unconditionally exits if params.input is unset. Because main.nf includes workflows/cutandrun.nf regardless of the selected entrypoint, invoking nextflow run main.nf -entry DIFFERENTIAL_ONLY --differential_from_run … without a samplesheet will hit the exit at load time and terminate before the differential-only workflow can start. The input check needs to be gated so it only runs when the CUTANDRUN workflow is actually executed.

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dhusmann · 2026-01-04T14:35:52Z

Fix for #2 (review)

Gate CUTANDRUN input samplesheet check so differential-only entrypoint can run without --input

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12859800)

dhusmann · 2026-01-04T14:35:58Z

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dhusmann · 2026-01-04T14:52:46Z

Fix for #2 (comment)

Join summary file list before passing to differential_summary.py so all summary TSVs are picked up

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12859903)

dhusmann · 2026-01-04T14:52:59Z

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dhusmann · 2026-01-04T15:15:53Z

Fix for #2 (comment)

Detect missing Java in span_diff.py and fall back with an explicit warning/reason instead of hard-failing
Added openjdk to the SPAN conda env for non-container runs

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12860059)

dhusmann · 2026-01-04T15:16:04Z

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cutandrun/workflows/cutandrun.nf

Lines 7 to 12 in 14e761e

    
           include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation' 
        
           // Validate input parameters in specialised library 
        
           WorkflowCutandrun.initialise(params, log) 
        
           def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs) 
        
           def citation = '\n' + WorkflowMain.citation(workflow) + '\n'

Differential-only entry still blocked by genome/gtf validation

The new DIFFERENTIAL_ONLY entrypoint can’t actually run without the full reference inputs because workflows/cutandrun.nf still invokes WorkflowCutandrun.initialise unconditionally. That initializer (lib/WorkflowCutandrun.groovy:25–36) errors out when params.fasta or params.gtf are unset, so running nextflow run main.nf -entry DIFFERENTIAL_ONLY --differential_from_run … --gene_bed … fails before the entry workflow starts unless users also supply a genome FASTA and GTF—inputs the entry was meant to avoid. Please gate the initialisation or relax those checks for the differential-only path so the new entry is usable with just the manifests/gene_bed it requires.

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dhusmann · 2026-01-04T15:35:17Z

Fix for #2 (comment)

Use the BED name column from the closest output (based on column counts) so nearest_gene_name/id are correct for bed12 and bed3 inputs

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12860193)

dhusmann · 2026-01-04T15:35:29Z

Fix for #2 (review)

Gate WorkflowCutandrun.initialise in workflows/cutandrun.nf so differential-only entry avoids genome/gtf validation

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12860193)

dhusmann · 2026-01-04T15:35:42Z

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dhusmann · 2026-01-04T16:02:38Z

Fix for #2 (comment)

Select SPAN peaks deterministically using the caller order from params.callers (fallback to sorted callers) and warn if multiple are present

Tests: pytest --keep-workflow-wd tests/test_07_differential.yml (SLURM 12860462)

dhusmann · 2026-01-04T16:03:02Z

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dhusmann · 2026-01-05T01:28:45Z

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dhusmann · 2026-01-05T04:56:01Z

Full pytest suite passed: 296 tests, 1 warning. Slurm job 12889297 COMPLETED 0:0 (02:43:02). Log: /scratch/users/dhusmann/runs/pytest_full/20260104_181233/logs/pytest_full_12889297.out

dhusmann · 2026-01-09T09:40:28Z

Normalization tweak in bc423f2.\n\n- When spike-in/MS scaling is applied, CPM is now skipped (scaling becomes the normalization), and applied_steps reflects that; this avoids cancellation/double-scaling while keeping factors effective (#2 (comment)).

dhusmann · 2026-01-09T09:40:51Z

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dhusmann · 2026-01-09T09:53:19Z

Cache lookup tweak in 687d16d.\n\n- differential-only now accepts cached chipbinner windows even if --blacklist isn’t provided, by only enforcing the hash match when a blacklist path is set (#2 (comment)).

dhusmann · 2026-01-09T09:53:44Z

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dhusmann · 2026-01-09T10:08:28Z

Spike-in validation in d3d4c9e.\n\n- ChIPBinner now errors (allow_partial -> SKIP) if --use-spikein is set and any sample is missing a spikein_scale_factor, preventing mixed scaling states (#2 (comment)).

dhusmann · 2026-01-09T10:08:52Z

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dhusmann · 2026-01-09T10:21:48Z

Allow-partial fix in dd781b6.\n\n- Window lookup now happens inside the try/except so missing/invalid windows fall back to SKIP when --allow-partial is set (#2 (comment)).

dhusmann · 2026-01-09T10:22:13Z

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dhusmann · 2026-01-09T10:32:56Z

Posthoc spike-in auto fix in 4725d67.\n\n- When differential_use_spikein=auto in posthoc mode, we now infer Spikein vs non-Spikein from the manifest normalisation_mode column and broadcast that value to DiffBind/ChIPBinner/SPAN (#2 (comment)).

dhusmann · 2026-01-09T10:33:25Z

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dhusmann · 2026-01-10T00:34:23Z

Fixes review items in 865bd9b: normalize SKIPPED→SKIP in differential summaries, add per-method MultiQC tables (chipbinner/span), validate --mode in span_diff.py, and avoid Channel redefinition in differential_peak_calling. The remote --gene_bed handling in differential-only was already fixed in c86079c (file() + gunzip), so that thread is resolved as well. Addresses #2 (comment) and #2 (comment).

dhusmann · 2026-01-10T00:34:41Z

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dhusmann · 2026-01-12T11:11:14Z

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

Branch: differential_peak_calling_2
Commit: a64a69c

Most recent test-history entry (docs/test_history/differential_peak_calling_2.md):

2026-01-12 — pytest-suite (Slurm)

JobID: 13250786
Run dir: /scratch/users/dhusmann/runs/pytest-suite/20260111_183752
Result: COMPLETED 0:0

dhusmann · 2026-01-13T03:07:51Z

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Add differential peak calling extension

7611f07

chatgpt-codex-connector Bot reviewed Jan 4, 2026

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Comment thread bin/diffbind_run.R

Apply diffbind extra params

d7bddb2

chatgpt-codex-connector Bot reviewed Jan 4, 2026

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Gate input check for differential-only entry

32264bc

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Comment thread modules/local/differential_summary.nf

Fix differential summary inputs

528d3f9

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Comment thread bin/span_diff.py Outdated

Handle missing Java for SPAN native mode

14e761e

chatgpt-codex-connector Bot reviewed Jan 4, 2026

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Comment thread bin/annotate_regions.py Outdated

Fix differential-only init and annotation

315dcc6

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Comment thread subworkflows/local/differential_peak_calling.nf Outdated

Deterministic SPAN peak selection

17fa79c

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Comment thread lib/WorkflowMain.groovy

Skip CPM when scaling applied

bc423f2

chatgpt-codex-connector Bot reviewed Jan 9, 2026

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Comment thread workflows/differential_only.nf Outdated

Relax cached windows blacklist matching

687d16d

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Comment thread bin/chipbinner_run.py

Require spike-in factors when enabled

d3d4c9e

chatgpt-codex-connector Bot reviewed Jan 9, 2026

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Comment thread bin/chipbinner_run.py Outdated

Allow partial on windows lookup

dd781b6

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Comment thread subworkflows/local/differential_peak_calling.nf Outdated

Derive spike-in usage from manifests

4725d67

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Comment thread bin/span_diff.py Outdated

Fix differential summary normalization and SPAN mode validation

865bd9b

dhusmann added 2 commits January 12, 2026 03:09

Update differential workflow outputs and tests

b3341a6

Record pytest suite history for differential_peak_calling_2

a64a69c

Guard spike-in broadcast for scalar values

2b09152

	// Check mandatory parameters that cannot be checked in the groovy lib as we want a channel for them
	if (params.input) { ch_input = file(params.input) } else { exit 1, "Input samplesheet not specified!" }

	include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'

	// Validate input parameters in specialised library
	WorkflowCutandrun.initialise(params, log)
	def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
	def citation = '\n' + WorkflowMain.citation(workflow) + '\n'

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dhusmann commented Jan 4, 2026

Summary

Testing

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