From 2d35145d0a35116056ca9577446aa7bf176dd465 Mon Sep 17 00:00:00 2001 From: Ido Bar Date: Fri, 2 Apr 2021 04:23:11 +1000 Subject: [PATCH 1/3] Fix mapdamage_rescaling naming of output bam files Use `${bam.basename}` (or `${base}`, which was already defined but not used) to strip the `.bam` extension of the original input file for the output of `mapdamage_rescaling`, so filenames won't turn up like this: ``` library_libmerged_rg_rmdup.bam_rescaled.bam ``` --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index f3ad4b2a0..fd998ebef 100644 --- a/main.nf +++ b/main.nf @@ -2081,8 +2081,8 @@ process mapdamage_rescaling { def singlestranded = strandedness == "single" ? '--single-stranded' : '' def size = params.large_ref ? '-c' : '' """ - mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out ${bam}_rescaled.bam --rescale-length-5p ${params.rescale_length_5p} --rescale-length-3p=${params.rescale_length_3p} ${singlestranded} - samtools index ${bam}_rescaled.bam ${size} + mapDamage -i ${bam} -r ${fasta} --rescale --rescale-out ${base}_rescaled.bam --rescale-length-5p ${params.rescale_length_5p} --rescale-length-3p=${params.rescale_length_3p} ${singlestranded} + samtools index ${base}_rescaled.bam ${size} """ } From 16b4b574d59e757a0e22caf19a57a251fe9ac859 Mon Sep 17 00:00:00 2001 From: IdoBar Date: Fri, 2 Apr 2021 05:13:14 +1000 Subject: [PATCH 2/3] Updated CHANGELOG.md to reflect changes --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 348aa7562..853c7df7f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` +- Fix filename for bam output of `mapdamage_rescaling` - [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command - Fixed some Java tools not following process memory specifications - Updated template to nf-core/tools 1.13.2 From 61e471aa39984593458715e555b4d7adfc1af21b Mon Sep 17 00:00:00 2001 From: Ido Bar Date: Fri, 2 Apr 2021 05:21:02 +1000 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 853c7df7f..86848e4f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` -- Fix filename for bam output of `mapdamage_rescaling` +- [#719](https://github.com/nf-core/eager/pull/719) - Fix filename for bam output of `mapdamage_rescaling` - [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command - Fixed some Java tools not following process memory specifications - Updated template to nf-core/tools 1.13.2