From 335396ae78c48efc66f746e791e409d9a2fad1de Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 20 Jul 2022 13:14:44 +0200 Subject: [PATCH 1/2] fix path to file in csv files --- subworkflows/local/mapping_csv.nf | 4 ++-- subworkflows/local/markduplicates_csv.nf | 4 ++-- subworkflows/local/prepare_recalibration_csv.nf | 6 +++--- subworkflows/local/recalibrate_csv.nf | 4 ++-- subworkflows/local/variantcalling_csv.nf | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/subworkflows/local/mapping_csv.nf b/subworkflows/local/mapping_csv.nf index 1c0d5ae094..b43e5fd96d 100644 --- a/subworkflows/local/mapping_csv.nf +++ b/subworkflows/local/mapping_csv.nf @@ -13,8 +13,8 @@ workflow MAPPING_CSV { sample = meta.sample sex = meta.sex status = meta.status - bam = "${params.outdir}/preprocessing/${sample}/mapped/${bam.name}" - bai = "${params.outdir}/preprocessing/${sample}/mapped/${bai.name}" + bam = "${params.outdir}/preprocessing/mapped/${sample}/${bam.name}" + bai = "${params.outdir}/preprocessing/mapped/${sample}/${bai.name}" ["mapped.csv", "patient,sex,status,sample,bam,bai\n${patient},${sex},${status},${sample},${bam},${bai}\n"] } } diff --git a/subworkflows/local/markduplicates_csv.nf b/subworkflows/local/markduplicates_csv.nf index 0819153351..b214cdc50f 100644 --- a/subworkflows/local/markduplicates_csv.nf +++ b/subworkflows/local/markduplicates_csv.nf @@ -15,8 +15,8 @@ workflow MARKDUPLICATES_CSV { status = meta.status suffix_aligned = params.save_output_as_bam ? "bam" : "cram" suffix_index = params.save_output_as_bam ? "bam.bai" : "cram.crai" - file = "${params.outdir}/preprocessing/${sample}/markduplicates/${file.baseName}.${suffix_aligned}" - index = "${params.outdir}/preprocessing/${sample}/markduplicates/${index.baseName.minus(".cram")}.${suffix_index}" + file = "${params.outdir}/preprocessing/markduplicates/${sample}/${file.baseName}.${suffix_aligned}" + index = "${params.outdir}/preprocessing/markduplicates/${sample}/${index.baseName.minus(".cram")}.${suffix_index}" ["markduplicates_no_table.csv", "patient,sex,status,sample,cram,crai\n${patient},${sex},${status},${sample},${file},${index}\n"] } } diff --git a/subworkflows/local/prepare_recalibration_csv.nf b/subworkflows/local/prepare_recalibration_csv.nf index c35a821545..e65d3ba07b 100644 --- a/subworkflows/local/prepare_recalibration_csv.nf +++ b/subworkflows/local/prepare_recalibration_csv.nf @@ -17,9 +17,9 @@ workflow PREPARE_RECALIBRATION_CSV { status = meta.status suffix_aligned = params.save_output_as_bam ? "bam" : "cram" suffix_index = params.save_output_as_bam ? "bam.bai" : "cram.crai" - cram = "${params.outdir}/preprocessing/${sample}/markduplicates/${cram.baseName}.${suffix_aligned}" - crai = "${params.outdir}/preprocessing/${sample}/markduplicates/${crai.baseName.minus(".cram")}.${suffix_index}" - table = "${params.outdir}/preprocessing/${sample}/recal_table/${sample}.recal.table" + cram = "${params.outdir}/preprocessing/markduplicates/${sample}/${cram.baseName}.${suffix_aligned}" + crai = "${params.outdir}/preprocessing/markduplicates/${sample}/${crai.baseName.minus(".cram")}.${suffix_index}" + table = "${params.outdir}/preprocessing/recal_table/${sample}/${sample}.recal.table" ["markduplicates.csv", "patient,sex,status,sample,cram,crai,table\n${patient},${sex},${status},${sample},${cram},${crai},${table}\n"] } } else { diff --git a/subworkflows/local/recalibrate_csv.nf b/subworkflows/local/recalibrate_csv.nf index e5068e6928..bbf5625ff5 100644 --- a/subworkflows/local/recalibrate_csv.nf +++ b/subworkflows/local/recalibrate_csv.nf @@ -13,8 +13,8 @@ workflow RECALIBRATE_CSV { sample = meta.sample sex = meta.sex status = meta.status - file = "${params.outdir}/preprocessing/${sample}/recalibrated/${file.name}" - index = "${params.outdir}/preprocessing/${sample}/recalibrated/${index.name}" + file = "${params.outdir}/preprocessing/recalibrated/${sample}/${file.name}" + index = "${params.outdir}/preprocessing/recalibrated/${sample}/${index.name}" ["recalibrated.csv", "patient,sex,status,sample,cram,crai\n${patient},${sex},${status},${sample},${file},${index}\n"] } } diff --git a/subworkflows/local/variantcalling_csv.nf b/subworkflows/local/variantcalling_csv.nf index 0382126ae0..99e9beb97d 100644 --- a/subworkflows/local/variantcalling_csv.nf +++ b/subworkflows/local/variantcalling_csv.nf @@ -12,7 +12,7 @@ workflow VARIANTCALLING_CSV { patient = meta.patient sample = meta.id variantcaller = meta.variantcaller - vcf = "${params.outdir}/variant_calling/${meta.id}/${variantcaller}/${vcf.getName()}" + vcf = "${params.outdir}/variant_calling/${variantcaller}/${meta.id}/${vcf.getName()}" ["variantcalled.csv", "patient,sample,variantcaller,vcf\n${patient},${sample},${variantcaller},${vcf}\n"] } } From a36e6973a4c662b3a1d0597f23f8608514f0636f Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Wed, 20 Jul 2022 13:17:55 +0200 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2eb53284d2..34efdf8126 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -154,6 +154,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#655](https://github.com/nf-core/sarek/pull/655) - Fix `--intervals false` logic & add versioning for local modules - [#658](https://github.com/nf-core/sarek/pull/658) - Fix split fastq names in multiqc-report - [#666](https://github.com/nf-core/sarek/pull/666) - Simplify multiqc config channel input +- [#669](https://github.com/nf-core/sarek/pull/669) - Fix path to files when creating csv files ### Deprecated