From 0dc940825a0553c1059793c79de6e55de2cde848 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Oct 2024 12:14:10 +0200 Subject: [PATCH 1/4] Remove _REP from id for posterior grouping --- .../bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf b/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf index 294a0eec..f1cf7212 100644 --- a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf +++ b/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 { From 75acca430e35949ebc5d3b9a8112963b24cf92b0 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Oct 2024 12:14:19 +0200 Subject: [PATCH 2/4] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index cdde3c09..e02dc561 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 #418](https://github.com/nf-core/chipseq/pull/418)] - Fix bug on how replicates are set for MACS3 downstream analysis. ### Parameters From 5850c6c9bebe246ae81b55614859fdf7a013ccb9 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Oct 2024 12:20:57 +0200 Subject: [PATCH 3/4] Fix changelog and update release date --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e02dc561..95ccb133 100644 --- a/CHANGELOG.md +++ b/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 @@ -48,7 +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 #418](https://github.com/nf-core/chipseq/pull/418)] - Fix bug on how replicates are set for MACS3 downstream analysis. +- [[PR #420](https://github.com/nf-core/chipseq/pull/420)] - Fix bug on how replicates are set for MACS3 downstream analysis. ### Parameters From a950571a56ce3dab8cd6c59a8e0915146469bd31 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 7 Oct 2024 14:33:01 +0200 Subject: [PATCH 4/4] Fix how groups are count --- .../bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf b/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf index f1cf7212..54a6eee8 100644 --- a/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf +++ b/subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf @@ -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 }