Merge pull request #669 from maxulysse/dev_restart_csv

fix path to file in csv files

Author: maxulysse

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
 

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"]
         }
 }

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"]
         }
 }

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 {

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"]
         }
 }

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"]
         }
 }