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dhusmann / cutandrun Public

forked from nf-core/cutandrun

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Adding new peak callers#5

Open

dhusmann wants to merge 19 commits into

differential_peak_callingdhusmann/cutandrun:differential_peak_callingfrom

adding_new_peak_callersdhusmann/cutandrun:adding_new_peak_callersCopy head branch name to clipboard

Conversation Commits19 (19)Checks Files changed

Open

Adding new peak callers#5
dhusmann wants to merge 19 commits into
differential_peak_callingfrom
adding_new_peak_callers

Commits

Commits on Jan 5, 2026

Enforce control matching and record pooling fallbacks
dhusmann
committed
Always emit spike-in normalisation factor reports
dhusmann
committed
Expand peak QC across callers
dhusmann
committed
Align peak outputs to biological sample IDs
dhusmann
committed
Support consensus_grouping all
dhusmann
committed
Add CI tests for control validation and QC
dhusmann
committed
Fix control fallback handling and sample IDs
dhusmann
committed
Fix samplesheet warnings and multi-caller FRiP
dhusmann
committed

Commits on Jan 9, 2026

Avoid dropping targets when control group missing
dhusmann
committed
Clarify control-missing warnings
dhusmann
committed
Fix multi-caller heatmap joins
dhusmann
committed

Commits on Jan 10, 2026

Fix channel redefinition in peak_calling_extended
dhusmann
committed
Record pytest-suite run 2026-01-09
dhusmann
committed

Commits on Jan 20, 2026

Fix SPAN outputs and peak QC bedtools
dhusmann
committed
Fix peak QC repro intersect format
dhusmann
committed

Commits on Jan 21, 2026

Harden dumpsoftwareversions + bump frag len mem
dhusmann
committed
Fix FRiP awk computation
dhusmann
committed
Fix callers init and pre-dedup stats for peak prep
dhusmann
committed
Avoid MultiQC collisions for peak reproducibility
dhusmann
committed

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