Merge pull request #1108 from maxulysse/remove_minus

FIX: Refactor prefix definition
nf-core · Jun 14, 2023 · abc7fe6 · abc7fe6
2 parents 875faee + 6276707
commit abc7fe6
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Showing 5 changed files with 9 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -31,6 +31,7 @@ Vuoinesluobbalah is a lake close to Bierikjávrre.
 - [#1101](https://github.com/nf-core/sarek/pull/1101) - Remove duplicate index computation for GATK4 Markduplicates & [#1065](https://github.com/nf-core/sarek/issues/1065)
 - [#1101](https://github.com/nf-core/sarek/pull/1101) - Fix GATK4 version for GATK4 MarkduplicatesSpark [#1068](https://github.com/nf-core/sarek/issues/1068)
 - [#1105](https://github.com/nf-core/sarek/pull/1105) - Remove `params.tracedir`
+- [#1108](https://github.com/nf-core/sarek/pull/1108) - Refactor bad prefix definition for vcf files [#938](https://github.com/nf-core/sarek/issues/938)
 
 ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure
 

diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config
@@ -18,7 +18,7 @@ process {
     // SNPEFF
     if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
         withName: 'SNPEFF_SNPEFF' {
-            ext.prefix       = { "${vcf.baseName.minus(".vcf")}_snpEff" }
+            ext.prefix       = { vcf.baseName - ".vcf" + "_snpEff" }
             ext.args         = '-nodownload -canon -v'
             if (!params.snpeff_cache && !params.download_cache) container = { params.snpeff_genome ? "docker.io/nfcore/snpeff:${params.snpeff_version}.${params.snpeff_genome}" : "docker.io/nfcore/snpeff:${params.snpeff_version}.${params.genome}" }
             publishDir       = [
@@ -46,7 +46,7 @@ process {
                 (params.vep_custom_args)                                              ?: ''
             ].join(' ').trim() }
             // If just VEP: <vcf prefix>_VEP.ann.vcf
-            ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP.ann" }
+            ext.prefix       = { vcf.baseName - ".vcf" + "_VEP.ann" }
             if (!params.vep_cache && !params.download_cache)    container = { params.vep_genome ? "docker.io/nfcore/vep:${params.vep_version}.${params.vep_genome}" : "docker.io/nfcore/vep:${params.vep_version}.${params.genome}" }
             publishDir       = [
                 [
@@ -67,14 +67,14 @@ process {
     if (params.tools && params.tools.split(',').contains('merge')) {
         withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP" {
             // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
-            ext.prefix       = { "${vcf.baseName.minus(".ann.vcf")}_VEP.ann" }
+            ext.prefix       = { vcf.baseName - ".ann.vcf" + "_VEP.ann" }
         }
     }
 
     // ALL ANNOTATION TOOLS
     if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
         withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)" {
-            ext.prefix       = { input.baseName.minus(".vcf") }
+            ext.prefix       = { input.name - ".vcf" }
             publishDir       = [
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },

diff --git a/conf/modules/freebayes.config b/conf/modules/freebayes.config
@@ -35,7 +35,7 @@ process {
     }
 
     withName: 'BCFTOOLS_SORT' {
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }
+        ext.prefix       = { meta.num_intervals <= 1 ? meta.id + ".freebayes" : vcf.name - ".vcf" + ".sort" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },

diff --git a/conf/modules/joint_germline.config b/conf/modules/joint_germline.config
@@ -32,7 +32,7 @@ process {
 
     if (params.tools && params.tools.contains('haplotypecaller') && params.joint_germline) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT' {
-            ext.prefix       = { "${vcf.baseName.minus("vcf")}sort" }
+            ext.prefix       = { vcf.baseName - ".vcf" + ".sort" }
             publishDir       = [
                 enabled: false
             ]

diff --git a/conf/modules/modules.config b/conf/modules/modules.config
@@ -90,7 +90,7 @@ process {
     // VCF
     withName: 'BCFTOOLS_STATS' {
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('bcftools')) }
-        ext.prefix       = { "${vcf.baseName.minus(".vcf")}" }
+        ext.prefix       = { vcf.baseName - ".vcf" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/bcftools/${meta.variantcaller}/${meta.id}/" },
@@ -100,7 +100,7 @@ process {
 
     withName: 'VCFTOOLS_.*' {
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('vcftools')) }
-        ext.prefix       = { "${variant_file.baseName.minus(".vcf")}" }
+        ext.prefix       = { variant_file.baseName - ".vcf" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/vcftools/${meta.variantcaller}/${meta.id}/" },