Adding new peak callers

[dhusmann]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/cutandrun branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Preserve unique IDs for technical replicates

When a group/condition/replicate has multiple technical replicates (supported earlier in this function and shown in the docstring), this now assigns the same sample_id to every row. That produces duplicate id values in the validated samplesheet, and downstream code (including the new meta.sample_id prefixes in this commit) uses these IDs for joins and published filenames, so technical replicates will collide and overwrite each other or be joined ambiguously. To avoid losing replicate-specific outputs, keep a unique suffix (e.g., the previous T{idx}) or otherwise disambiguate each row’s ID.

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[dhusmann]

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

Branch: adding_new_peak_callers
Commit: 91f2ff4

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

2026-01-09 — pytest-suite (Slurm)

• JobID/run dir: 13170828 — /scratch/users/dhusmann/nextflow-work/runs/pytest-suite/20260109_183946
• Command: pytest-suite (pytest-workflow) --maxfail=1 --kwdof --symlink --ga --color=yes (via pytest_suite.sh)
• Result: 323 passed, 0 failed (2:05:41), SLURM COMPLETED 0:0
• Failures observed (prior attempt 13116667): Nextflow compile error "Variable ch_seacr_pairs/ch_macs_pairs already defined" in subworkflows/local/peak_calling_extended.nf; fix in 1491b92 (remove def on ch_*_inputs)