Merge pull request #420 from JoseEspinosa/updates

Fix how replicates are set for downstream analysis

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-02
+## [[2.1.0](https://github.com/nf-core/chipseq/releases/tag/2.1.0)] - 2024-10-07
 
 ### Credits
 
@@ -48,6 +48,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #406](https://github.com/nf-core/chipseq/pull/406)] - Update metro map to show macs3 instead of macs2.
 - [[#409](https://github.com/nf-core/chipseq/issues/409)] - Bulk modules and subworkflows update.
 - [[PR #415](https://github.com/nf-core/chipseq/pull/415)] - Get rid of `oras` in modules.
+- [[PR #420](https://github.com/nf-core/chipseq/pull/420)] - Fix bug on how replicates are set for MACS3 downstream analysis.
 
 ### Parameters
 

subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf

@@ -30,7 +30,7 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
     ch_peaks
         .map {
             meta, peak ->
-                [ meta.antibody, meta.id - ~/_T\d+$/, peak ]
+                [ meta.antibody, meta.id - ~/_REP\d+$/, peak ]
         }
         .groupTuple()
         .map {
@@ -46,7 +46,7 @@ workflow BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2 {
                 def meta_new = [:]
                 meta_new.id = antibody
                 meta_new.multiple_groups = groups.size() > 1
-                meta_new.replicates_exist = groups.max { groups.value }.value > 1
+                meta_new.replicates_exist = groups.max { it.value }.value > 1
                 [ meta_new, peaks ]
         }
         .set { ch_antibody_peaks }