From 19f79ef1504f2638d524fc9c4b0b6a32c509ee2d Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 14 Feb 2019 15:24:22 +0100 Subject: [PATCH 1/2] fix BAMQC output --- main.nf | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index c96b4cf82e..2016b462af 100644 --- a/main.nf +++ b/main.nf @@ -190,7 +190,7 @@ process RunBamQCmapped { set idPatient, status, idSample, idRun, file(bam) from mappedBamForQC output: - file(idSample) into bamQCmappedReport + file("${bam.baseName}") into bamQCmappedReport when: !params.noReports && !params.noBAMQC @@ -204,7 +204,7 @@ process RunBamQCmapped { -nt ${task.cpus} \ -skip-duplicated \ --skip-dup-mode 0 \ - -outdir ${idSample} \ + -outdir ${bam.baseName} \ -outformat HTML """ } @@ -459,7 +459,7 @@ process RunBamQCrecalibrated { set idPatient, status, idSample, file(bam), file(bai) from bamForBamQC output: - file(idSample) into bamQCrecalibratedReport + file("${bam.baseName}") into bamQCrecalibratedReport when: !params.noReports && !params.noBAMQC @@ -473,7 +473,7 @@ process RunBamQCrecalibrated { -nt ${task.cpus} \ -skip-duplicated \ --skip-dup-mode 0 \ - -outdir ${idSample} \ + -outdir ${bam.baseName} \ -outformat HTML """ } From 594ecda94223f9b041898dae90da5c139f0d623b Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 14 Feb 2019 15:30:42 +0100 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d20f79e54..3ff3db8272 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Fixed` - [#720](https://github.com/SciLifeLab/Sarek/pull/720) - bamQC is now run on the recalibrated bams, and not after MarkDuplicates +- [#727](https://github.com/SciLifeLab/Sarek/pull/727) - bamQC outputs are no longer overwritten (name of dir is now the file instead of sample) ## [2.2.2] - 2018-12-19