From 1e879750037945b7f1410060feef709bc43bd598 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Mon, 30 Sep 2024 11:52:59 +0200
Subject: [PATCH] simpligy tools logic

---
 conf/modules/aligner.config             |  8 +++----
 conf/modules/annotate.config            | 16 +++++++-------
 conf/modules/ascat.config               |  2 +-
 conf/modules/cnvkit.config              |  8 +++----
 conf/modules/controlfreec.config        |  2 +-
 conf/modules/deepvariant.config         |  2 +-
 conf/modules/download_cache.config      |  4 ++--
 conf/modules/freebayes.config           |  4 ++--
 conf/modules/haplotypecaller.config     |  4 ++--
 conf/modules/lofreq.config              |  4 ++--
 conf/modules/manta.config               |  2 +-
 conf/modules/markduplicates.config      | 14 ++++++-------
 conf/modules/modules.config             | 18 ++++++++--------
 conf/modules/mpileup.config             |  6 +++---
 conf/modules/mutect2.config             |  4 ++--
 conf/modules/ngscheckmate.config        |  2 +-
 conf/modules/prepare_genome.config      | 22 +++++++++----------
 conf/modules/recalibrate.config         |  2 +-
 conf/modules/sentieon_dedup.config      |  6 +++---
 conf/modules/sentieon_dnascope.config   |  2 +-
 conf/modules/sentieon_haplotyper.config |  2 +-
 conf/modules/strelka.config             |  2 +-
 conf/modules/tiddit.config              |  4 ++--
 workflows/sarek/main.nf                 | 28 ++++++++++++-------------
 24 files changed, 84 insertions(+), 84 deletions(-)

diff --git a/conf/modules/aligner.config b/conf/modules/aligner.config
index 5f44e199b0..cd8dfa773d 100644
--- a/conf/modules/aligner.config
+++ b/conf/modules/aligner.config
@@ -46,8 +46,8 @@ process {
                     if (params.save_output_as_bam &&
                         (
                             params.save_mapped ||
-                            (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
-                            !(params.tools && params.tools.split(',').contains('sentieon_dedup'))
+                            (params.skip_tools && params.skip_tools.contains('markduplicates')) &&
+                            !(params.tools && params.tools.contains('sentieon_dedup'))
                         ) && (meta.size * meta.num_lanes == 1)
                     ) { "mapped/${meta.id}/${it}" }
                     else { null }
@@ -60,7 +60,7 @@ process {
             // However if it's skipped, reads need to be coordinate-sorted
             // Only name sort if Spark for Markduplicates + duplicate marking is not skipped
             // Currently SENTIEON_BWAMEM only supports coordinate sorting the reads.
-            ext.args2  = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' }
+            ext.args2  = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.contains('markduplicates'))) ? '-n' : '' }
         }
 
         withName: 'BWAMEM.*_MEM|SENTIEON_BWAMEM' {
@@ -75,7 +75,7 @@ process {
             path: { "${params.outdir}/preprocessing/" },
             pattern: "*{bam,bai}",
             // Only save if (save_output_as_bam AND (no_markduplicates OR save_mapped ))
-            saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) ? "mapped/${meta.id}/${it}" : null }
+            saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.contains('markduplicates'))) ? "mapped/${meta.id}/${it}" : null }
         ]
     }
 
diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config
index b02c1b3ef3..626a25ee9a 100644
--- a/conf/modules/annotate.config
+++ b/conf/modules/annotate.config
@@ -16,7 +16,7 @@
 process {
 
     // SNPEFF
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
+    if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
         withName: 'SNPEFF_SNPEFF' {
             ext.args   = { '-nodownload -canon -v' }
             ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' }
@@ -25,14 +25,14 @@ process {
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
                     pattern: "*{csv,html,genes.txt}",
-                    saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
+                    saveAs: { params.tools.contains('snpeff') ? it : null }
                 ]
             ]
         }
     }
 
     // VEP
-    if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
+    if (params.tools && (params.tools.contains('vep') || params.tools.contains('merge'))) {
         withName: 'ENSEMBLVEP_VEP' {
             ext.args   = { [
                 "--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
@@ -62,7 +62,7 @@ process {
     }
 
     // BCFTOOLS ANNOTATE
-    if (params.tools && params.tools.split(',').contains('bcfann')) {
+    if (params.tools && params.tools.contains('bcfann')) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
             ext.args   = { '--output-type z' }
             ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
@@ -75,7 +75,7 @@ process {
     }
 
     // SNPEFF THEN VEP
-    if (params.tools && params.tools.split(',').contains('merge')) {
+    if (params.tools && params.tools.contains('merge')) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' {
             ext.args   = { [
                 "--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
@@ -93,7 +93,7 @@ process {
     }
 
     // ALL ANNOTATION TOOLS
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge') || params.tools.split(',').contains('bcfann'))) {
+    if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('vep') || params.tools.contains('merge') || params.tools.contains('bcfann'))) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
             ext.prefix = { input.name - '.vcf' }
             publishDir = [
@@ -104,13 +104,13 @@ process {
         }
     }
 
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
+    if (params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge'))) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' {
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
                 pattern: "*{gz,gz.tbi}",
-                saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
+                saveAs: { params.tools.contains('snpeff') ? it : null }
             ]
         }
     }
diff --git a/conf/modules/ascat.config b/conf/modules/ascat.config
index 4df9824274..fedf014e6c 100644
--- a/conf/modules/ascat.config
+++ b/conf/modules/ascat.config
@@ -27,7 +27,7 @@ process {
             "min_map_qual": params.ascat_min_map_qual
             ]
         }
-        ext.when   = { params.tools && params.tools.split(',').contains('ascat') }
+        ext.when   = { params.tools && params.tools.contains('ascat') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/ascat/${meta.id}/" },
diff --git a/conf/modules/cnvkit.config b/conf/modules/cnvkit.config
index 2bf455faa7..4a2be31bfe 100644
--- a/conf/modules/cnvkit.config
+++ b/conf/modules/cnvkit.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'CNVKIT_BATCH' {
         ext.args   = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" }
-        ext.when   = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when   = { params.tools && params.tools.contains('cnvkit') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
@@ -26,7 +26,7 @@ process {
     }
 
     withName: '.*:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_CALL' {
-        ext.when   = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when   = { params.tools && params.tools.contains('cnvkit') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
@@ -47,7 +47,7 @@ process {
     withName: 'CNVKIT_EXPORT' {
         ext.args = "vcf"
         ext.prefix = { "${meta.id}.cnvcall" }
-        ext.when   = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when   = { params.tools && params.tools.contains('cnvkit') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
@@ -57,7 +57,7 @@ process {
 
     withName: 'CNVKIT_GENEMETRICS' {
         ext.prefix = { "${cnr.baseName}.genemetrics" }
-        ext.when   = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when   = { params.tools && params.tools.contains('cnvkit') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },
diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config
index b6fa043d0e..b4624c8609 100644
--- a/conf/modules/controlfreec.config
+++ b/conf/modules/controlfreec.config
@@ -24,7 +24,7 @@ process {
     }
 
     withName: 'FREEC_.*' {
-        ext.when   = { params.tools && params.tools.split(',').contains('controlfreec') }
+        ext.when   = { params.tools && params.tools.contains('controlfreec') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },
diff --git a/conf/modules/deepvariant.config b/conf/modules/deepvariant.config
index 021990f7f6..c730c48aec 100644
--- a/conf/modules/deepvariant.config
+++ b/conf/modules/deepvariant.config
@@ -18,7 +18,7 @@ process {
     withName: 'DEEPVARIANT' {
         ext.args   = { params.wes ?  "--model_type WES" : "--model_type WGS" }
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.baseName}" }
-        ext.when   = { params.tools && params.tools.split(',').contains('deepvariant') }
+        ext.when   = { params.tools && params.tools.contains('deepvariant') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
diff --git a/conf/modules/download_cache.config b/conf/modules/download_cache.config
index 5b36ab4cc5..189a1bcf7d 100644
--- a/conf/modules/download_cache.config
+++ b/conf/modules/download_cache.config
@@ -17,7 +17,7 @@ process {
 
     // SNPEFF
     withName: 'SNPEFF_DOWNLOAD' {
-        ext.when   = { params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge')) }
+        ext.when   = { params.tools && (params.tools.contains('snpeff') || params.tools.contains('merge')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { params.outdir_cache ? "${params.outdir_cache}/": "${params.outdir}/cache/" }
@@ -26,7 +26,7 @@ process {
 
     // VEP
     withName: 'ENSEMBLVEP_DOWNLOAD' {
-        ext.when   = { params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge')) }
+        ext.when   = { params.tools && (params.tools.contains('vep') || params.tools.contains('merge')) }
         ext.args   = { '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' }
         publishDir = [
             mode: params.publish_dir_mode,
diff --git a/conf/modules/freebayes.config b/conf/modules/freebayes.config
index 2c224aeffd..4d718f8c63 100644
--- a/conf/modules/freebayes.config
+++ b/conf/modules/freebayes.config
@@ -28,7 +28,7 @@ process {
         ext.args   = { '--min-alternate-fraction 0.1 --min-mapping-quality 1' }
         //To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.baseName}" }
-        ext.when   = { params.tools && params.tools.split(',').contains('freebayes') }
+        ext.when   = { params.tools && params.tools.contains('freebayes') }
         publishDir = [
             enabled: false
         ]
@@ -53,7 +53,7 @@ process {
     }
 
     // PAIR_VARIANT_CALLING
-    if (params.tools && params.tools.split(',').contains('freebayes')) {
+    if (params.tools && params.tools.contains('freebayes')) {
         withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
             ext.args = { "--pooled-continuous \
                             --pooled-discrete \
diff --git a/conf/modules/haplotypecaller.config b/conf/modules/haplotypecaller.config
index d5b8a3db40..8ec2c0613d 100644
--- a/conf/modules/haplotypecaller.config
+++ b/conf/modules/haplotypecaller.config
@@ -18,7 +18,7 @@ process {
     withName: 'GATK4_HAPLOTYPECALLER' {
         ext.args   = { params.joint_germline ? "-ERC GVCF" : "" }
         ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.baseName}.g" :"${meta.id}.haplotypecaller.${intervals.baseName}" ) }
-        ext.when   = { params.tools && params.tools.split(',').contains('haplotypecaller') }
+        ext.when   = { params.tools && params.tools.contains('haplotypecaller') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/"},
@@ -53,7 +53,7 @@ process {
         ]
     }
 
-    if (params.tools && params.tools.split(',').contains('haplotypecaller')) {
+    if (params.tools && params.tools.contains('haplotypecaller')) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' {
             ext.prefix = { "${meta.id}.realigned" }
             publishDir = [
diff --git a/conf/modules/lofreq.config b/conf/modules/lofreq.config
index 253b252b3b..53d86fd7ee 100644
--- a/conf/modules/lofreq.config
+++ b/conf/modules/lofreq.config
@@ -14,12 +14,12 @@
 //LOFREQ
 
 process {
-    if (params.tools && params.tools.split(',').contains('lofreq')) {
+    if (params.tools && params.tools.contains('lofreq')) {
 
         withName: "LOFREQ_CALLPARALLEL" {
             ext.args = { "--call-indels" }
             ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.lofreq" : "${meta.id}.lofreq.${intervals.baseName}" }
-            ext.when   = { params.tools && params.tools.split(',').contains('lofreq') }
+            ext.when   = { params.tools && params.tools.contains('lofreq') }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/variant_calling/" },
diff --git a/conf/modules/manta.config b/conf/modules/manta.config
index 71a1c43299..2816a27bc8 100644
--- a/conf/modules/manta.config
+++ b/conf/modules/manta.config
@@ -14,7 +14,7 @@
 // MANTA
 
 process {
-    if (params.tools && params.tools.split(',').contains('manta')) {
+    if (params.tools && params.tools.contains('manta')) {
         withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
             ext.args   = { params.wes ? "--exome" : '' }
             ext.prefix = { "${meta.id}.manta" }
diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config
index 55f29ede51..b130672d65 100644
--- a/conf/modules/markduplicates.config
+++ b/conf/modules/markduplicates.config
@@ -35,7 +35,7 @@ process {
 
     withName: 'NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' {
         ext.prefix = { "${meta.id}.md.cram" }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/samtools/${meta.id}" },
@@ -48,8 +48,8 @@ process {
         // Run only when mapping should be saved as CRAM or when no MD is done
         ext.when   = (params.save_mapped && !params.save_output_as_bam) ||
             (
-                (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
-                !(params.tools && params.tools.split(',').contains('sentieon_dedup'))
+                (params.skip_tools && params.skip_tools.contains('markduplicates')) &&
+                !(params.tools && params.tools.contains('sentieon_dedup'))
             )
         publishDir = [
             // Never publish if BAM only should be published
@@ -62,7 +62,7 @@ process {
 
     withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
         ext.prefix = { "${meta.id}.md.cram" }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/markduplicates/${meta.id}" },
@@ -73,7 +73,7 @@ process {
     withName: 'GATK4_MARKDUPLICATES' {
         ext.args   = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT'
         ext.prefix = { "${meta.id}.md.cram" }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('markduplicates')) }
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -85,7 +85,7 @@ process {
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/reports/" },
                 pattern: "*metrics",
-                saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
+                saveAs: { !(params.skip_tools && params.skip_tools.contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
             ]
         ]
     }
@@ -113,7 +113,7 @@ process {
 
     withName: 'NFCORE_SAREK:SAREK:CRAM_TO_BAM' {
         ext.when   = { params.save_output_as_bam }
-        if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
+        if (params.tools && params.tools.contains('sentieon_dedup')) {
             ext.prefix = { "${meta.id}.dedup" }
             publishDir = [
                 mode: params.publish_dir_mode,
diff --git a/conf/modules/modules.config b/conf/modules/modules.config
index d87f97174f..c87f308ca8 100644
--- a/conf/modules/modules.config
+++ b/conf/modules/modules.config
@@ -21,7 +21,7 @@ process {
 // QC
     withName: 'FASTQC' {
         ext.args   = { '--quiet' }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('fastqc')) }
         publishDir = [
             [
                 path: { "${params.outdir}/reports/fastqc/${meta.id}" },
@@ -42,7 +42,7 @@ process {
 
     withName: 'NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS' {
         ext.prefix = { "${meta.id}.sorted.cram" }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/samtools/${meta.id}" },
@@ -60,15 +60,15 @@ process {
     withName: 'MOSDEPTH' {
         ext.args   = { !params.wes ? "-n --fast-mode --by 500" : ""}
         ext.prefix = {
-            if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
+            if (params.tools && params.tools.contains('sentieon_dedup')) {
                 "${meta.id}.dedup"
-            } else if (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) {
+            } else if (params.skip_tools && params.skip_tools.contains('markduplicates')) {
                 "${meta.id}.sorted"
             } else {
                 "${meta.id}.md"
             }
         }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('mosdepth')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/mosdepth/${meta.id}" },
@@ -76,14 +76,14 @@ process {
         ]
     }
 
-    if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
+    if (!(params.skip_tools && params.skip_tools.contains('baserecalibrator'))) {
         withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH' {
             ext.prefix = { "${meta.id}.recal" }
         }
 
         withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS' {
             ext.prefix = { "${meta.id}.recal.cram" }
-            ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+            ext.when   = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/reports/samtools/${meta.id}" },
@@ -95,7 +95,7 @@ process {
     // VCF
     withName: 'BCFTOOLS_STATS' {
         ext.prefix = { vcf.baseName - ".vcf" }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('bcftools')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('bcftools')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/bcftools/${meta.variantcaller}/${meta.id}/" },
@@ -105,7 +105,7 @@ process {
 
     withName: 'VCFTOOLS_.*' {
         ext.prefix = { variant_file.baseName - ".vcf" }
-        ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('vcftools')) }
+        ext.when   = { !(params.skip_tools && params.skip_tools.contains('vcftools')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/vcftools/${meta.variantcaller}/${meta.id}/" },
diff --git a/conf/modules/mpileup.config b/conf/modules/mpileup.config
index dbdfa27fec..0e6b092388 100644
--- a/conf/modules/mpileup.config
+++ b/conf/modules/mpileup.config
@@ -25,7 +25,7 @@ process {
         ext.args2  = { '--multiallelic-caller' }
         ext.args3  = { "-i 'count(GT==\"RR\")==0'" } // only report non homozygous reference variants
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.bcftools" : "${meta.id}_${intervals.baseName}.bcftools" }
-        ext.when   = { params.tools && params.tools.split(',').contains('mpileup') }
+        ext.when   = { params.tools && params.tools.contains('mpileup') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/bcftools/${meta.id}/" },
@@ -44,7 +44,7 @@ process {
     }
 
     withName: 'SAMTOOLS_MPILEUP' {
-        ext.when   = { params.tools && params.tools.split(',').contains('controlfreec') }
+        ext.when   = { params.tools && params.tools.contains('controlfreec') }
         publishDir = [
             enabled: false
         ]
@@ -52,7 +52,7 @@ process {
     }
 
 // PAIR_VARIANT_CALLING
-    if (params.tools && params.tools.split(',').contains('controlfreec')) {
+    if (params.tools && params.tools.contains('controlfreec')) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' {
             ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" }
         }
diff --git a/conf/modules/mutect2.config b/conf/modules/mutect2.config
index 5892437ddc..da709ff45c 100644
--- a/conf/modules/mutect2.config
+++ b/conf/modules/mutect2.config
@@ -14,12 +14,12 @@
 // MUTECT2
 
 process {
-    if (params.tools && params.tools.split(',').contains('mutect2')) {
+    if (params.tools && params.tools.contains('mutect2')) {
 
         withName: 'GATK4_MUTECT2' {
             ext.args   = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" }
             ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.baseName}" }
-            ext.when   = { params.tools && params.tools.split(',').contains('mutect2') }
+            ext.when   = { params.tools && params.tools.contains('mutect2') }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/variant_calling/" },
diff --git a/conf/modules/ngscheckmate.config b/conf/modules/ngscheckmate.config
index 4d35c94468..a60b22eead 100644
--- a/conf/modules/ngscheckmate.config
+++ b/conf/modules/ngscheckmate.config
@@ -4,7 +4,7 @@ process {
         ext.args2  = { '--no-version --ploidy 1 -c' }
         ext.args3  = { '--no-version' }
         ext.prefix = { "${meta.id}.ngscheckmate" }
-        ext.when   = { params.tools && params.tools.split(',').contains('ngscheckmate') }
+        ext.when   = { params.tools && params.tools.contains('ngscheckmate') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/ngscheckmate/vcfs" },
diff --git a/conf/modules/prepare_genome.config b/conf/modules/prepare_genome.config
index 1f57237be7..c69ea3b5d0 100644
--- a/conf/modules/prepare_genome.config
+++ b/conf/modules/prepare_genome.config
@@ -36,7 +36,7 @@ process {
     }
 
     withName: 'CNVKIT_ANTITARGET' {
-        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when         = { params.tools && params.tools.contains('cnvkit') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference" },
@@ -47,7 +47,7 @@ process {
 
     withName: 'CNVKIT_REFERENCE' {
         ext.prefix       = { 'cnvkit' }
-        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
+        ext.when         = { params.tools && params.tools.contains('cnvkit') && !params.cnvkit_reference }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference" },
@@ -77,7 +77,7 @@ process {
     }
 
     withName: 'MSISENSORPRO_SCAN' {
-        ext.when         = { params.tools && params.tools.split(',').contains('msisensorpro') }
+        ext.when         = { params.tools && params.tools.contains('msisensorpro') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/msi" },
@@ -97,7 +97,7 @@ process {
     }
 
     withName: 'TABIX_BCFTOOLS_ANNOTATIONS' {
-        ext.when         = { !params.bcftools_annotations_tbi && params.bcftools_annotations && params.tools && params.tools.split(',').contains('bcfann') }
+        ext.when         = { !params.bcftools_annotations_tbi && params.bcftools_annotations && params.tools && params.tools.contains('bcfann') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/bcfann" },
@@ -107,7 +107,7 @@ process {
     }
 
     withName: 'TABIX_DBSNP' {
-        ext.when         = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope') || params.tools.split(',').contains('mutect2'))) }
+        ext.when         = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.contains('controlfreec') || params.tools.contains('haplotypecaller') || params.tools.contains('sentieon_haplotyper') || params.tools.contains('sentieon_dnascope') || params.tools.contains('mutect2'))) }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/dbsnp" },
@@ -117,7 +117,7 @@ process {
     }
 
     withName: 'TABIX_GERMLINE_RESOURCE' {
-        ext.when         = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') }
+        ext.when         = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.contains('mutect2') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/germline_resource" },
@@ -127,7 +127,7 @@ process {
     }
 
     withName: 'TABIX_KNOWN_INDELS' {
-        ext.when         = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
+        ext.when         = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.contains('haplotypecaller') || params.tools.contains('sentieon_haplotyper') || params.tools.contains('sentieon_dnascope'))) ) }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/known_indels" },
@@ -137,7 +137,7 @@ process {
     }
 
     withName: 'TABIX_KNOWN_SNPS' {
-        ext.when         = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
+        ext.when         = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.contains('haplotypecaller') || params.tools.contains('sentieon_haplotyper') )) ) }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/known_snps" },
@@ -147,7 +147,7 @@ process {
     }
 
     withName: 'TABIX_PON' {
-        ext.when         = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') }
+        ext.when         = { !params.pon_tbi && params.pon && params.tools && params.tools.contains('mutect2') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/pon" },
@@ -157,7 +157,7 @@ process {
     }
 
     withName: 'UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT' {
-        ext.when         = { params.tools && params.tools.split(',').contains('ascat')}
+        ext.when         = { params.tools && params.tools.contains('ascat')}
         publishDir       = [
             enabled: false
         ]
@@ -165,7 +165,7 @@ process {
 
     withName: 'UNTAR_CHR_DIR' {
         ext.prefix       = 'chr_dir'
-        ext.when         = { params.tools && params.tools.split(',').contains('controlfreec')}
+        ext.when         = { params.tools && params.tools.contains('controlfreec')}
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reference/" },
diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config
index 19bbb17d35..fa57c40b1e 100644
--- a/conf/modules/recalibrate.config
+++ b/conf/modules/recalibrate.config
@@ -28,7 +28,7 @@ process {
         ]
     }
 
-    if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
+    if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.contains('baserecalibrator')))) {
         withName: 'NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM' {
             ext.prefix       = { "${meta.id}.recal" }
             ext.when         = { meta.num_intervals > 1 }
diff --git a/conf/modules/sentieon_dedup.config b/conf/modules/sentieon_dedup.config
index df52c3bb95..9dbfd31045 100644
--- a/conf/modules/sentieon_dedup.config
+++ b/conf/modules/sentieon_dedup.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'SENTIEON_DEDUP' {
         ext.prefix       = { "${meta.id}.dedup" }
-        ext.when         = { params.tools && params.tools.split(',').contains('sentieon_dedup') }
+        ext.when         = { params.tools && params.tools.contains('sentieon_dedup') }
         publishDir       = [
             [
                 mode: params.publish_dir_mode,
@@ -29,14 +29,14 @@ process {
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/reports/" },
                 pattern: "*{metrics,metrics.multiqc.tsv}",
-                saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('sentieon_dedup_report')) ? "sentieon_dedup/${meta.id}/${it}" : null}
+                saveAs: { !(params.skip_tools && params.skip_tools.contains('sentieon_dedup_report')) ? "sentieon_dedup/${meta.id}/${it}" : null}
             ]
         ]
     }
 
     if (params.tools && params.tools.contains('sentieon_dedup')) {
         withName: 'NFCORE_SAREK:SAREK:BAM_SENTIEON_DEDUP:CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' {
-            ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+            ext.when         = { !(params.skip_tools && params.skip_tools.contains('samtools')) }
             ext.prefix       = { "${meta.id}.dedup.cram" }
             publishDir       = [
                 mode: params.publish_dir_mode,
diff --git a/conf/modules/sentieon_dnascope.config b/conf/modules/sentieon_dnascope.config
index 50cf373ea8..6100cab507 100644
--- a/conf/modules/sentieon_dnascope.config
+++ b/conf/modules/sentieon_dnascope.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'SENTIEON_DNASCOPE' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.dnascope" : "${meta.id}.dnascope.${intervals.baseName}" }
-        ext.when         = { params.tools && params.tools.split(',').contains('sentieon_dnascope') }
+        ext.when         = { params.tools && params.tools.contains('sentieon_dnascope') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/"},
diff --git a/conf/modules/sentieon_haplotyper.config b/conf/modules/sentieon_haplotyper.config
index c2b9582223..66bf02b7e0 100644
--- a/conf/modules/sentieon_haplotyper.config
+++ b/conf/modules/sentieon_haplotyper.config
@@ -17,7 +17,7 @@ process {
 
     withName: 'SENTIEON_HAPLOTYPER' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.haplotyper" : "${meta.id}.haplotyper.${intervals.baseName}" }
-        ext.when         = { params.tools && params.tools.split(',').contains('sentieon_haplotyper') }
+        ext.when         = { params.tools && params.tools.contains('sentieon_haplotyper') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/"},
diff --git a/conf/modules/strelka.config b/conf/modules/strelka.config
index badffb5df8..1e305275b6 100644
--- a/conf/modules/strelka.config
+++ b/conf/modules/strelka.config
@@ -18,7 +18,7 @@ process {
     withName: 'STRELKA_.*' {
         ext.args   = { params.wes ? '--exome' : '' }
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.baseName}" }
-        ext.when   = { params.tools && params.tools.split(',').contains('strelka') }
+        ext.when   = { params.tools && params.tools.contains('strelka') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
diff --git a/conf/modules/tiddit.config b/conf/modules/tiddit.config
index 335ecf0951..da04d5deb0 100644
--- a/conf/modules/tiddit.config
+++ b/conf/modules/tiddit.config
@@ -18,7 +18,7 @@ process {
     withName: 'TIDDIT_SV' {
         ext.args   = { bwa_index ? '' : '--skip_assembly' }
         ext.prefix = { "${meta.id}.tiddit" }
-        ext.when   = { params.tools && params.tools.split(',').contains('tiddit') }
+        ext.when   = { params.tools && params.tools.contains('tiddit') }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },
@@ -36,7 +36,7 @@ process {
     }
 
     // PAIR_VARIANT_CALLING
-    if (params.tools && params.tools.split(',').contains('tiddit')) {
+    if (params.tools && params.tools.contains('tiddit')) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
             ext.prefix = {"${meta.id}.tiddit.normal"}
         }
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
index 90307f19c2..b95a6ecfbf 100644
--- a/workflows/sarek/main.nf
+++ b/workflows/sarek/main.nf
@@ -204,7 +204,7 @@ workflow SAREK {
         // Additional options to be set up
 
         // QC
-        if (!(params.skip_tools && params.skip_tools.split(',').contains('fastqc'))) {
+        if (!(params.skip_tools && params.skip_tools.contains('fastqc'))) {
             FASTQC(input_fastq)
 
             reports = reports.mix(FASTQC.out.zip.collect{ meta, logs -> logs })
@@ -337,8 +337,8 @@ workflow SAREK {
         if (
             params.save_mapped ||
             (
-                (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
-                !(params.tools && params.tools.split(',').contains('sentieon_dedup'))
+                (params.skip_tools && params.skip_tools.contains('markduplicates')) &&
+                !(params.tools && params.tools.contains('sentieon_dedup'))
             )
         ) {
             // bams are merged (when multiple lanes from the same sample), indexed and then converted to cram
@@ -380,8 +380,8 @@ workflow SAREK {
 
         if (
             params.skip_tools &&
-            params.skip_tools.split(',').contains('markduplicates') &&
-            !(params.tools && params.tools.split(',').contains('sentieon_dedup'))
+            params.skip_tools.contains('markduplicates') &&
+            !(params.tools && params.tools.contains('sentieon_dedup'))
         ) {
             if (params.step == 'mapping') {
                 cram_skip_markduplicates = BAM_TO_CRAM_MAPPING.out.cram.join(BAM_TO_CRAM_MAPPING.out.crai, failOnDuplicate: true, failOnMismatch: true)
@@ -419,7 +419,7 @@ workflow SAREK {
 
             // Gather used softwares versions
             versions = versions.mix(BAM_MARKDUPLICATES_SPARK.out.versions)
-        } else if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
+        } else if (params.tools && params.tools.contains('sentieon_dedup')) {
             crai_for_markduplicates = params.step == 'mapping' ? bai_mapped : input_sample.map{ meta, input, index -> [ meta, index ] }
             BAM_SENTIEON_DEDUP(
                 cram_for_markduplicates,
@@ -466,7 +466,7 @@ workflow SAREK {
 
         // CSV should be written for the file actually out, either CRAM or BAM
         // Create CSV to restart from this step
-        csv_subfolder = (params.tools && params.tools.split(',').contains('sentieon_dedup')) ? 'sentieon_dedup' : 'markduplicates'
+        csv_subfolder = (params.tools && params.tools.contains('sentieon_dedup')) ? 'sentieon_dedup' : 'markduplicates'
 
         if (params.save_output_as_bam) CHANNEL_MARKDUPLICATES_CREATE_CSV(CRAM_TO_BAM.out.bam.join(CRAM_TO_BAM.out.bai, failOnDuplicate: true, failOnMismatch: true), csv_subfolder, params.outdir, params.save_output_as_bam)
         else CHANNEL_MARKDUPLICATES_CREATE_CSV(ch_md_cram_for_restart, csv_subfolder, params.outdir, params.save_output_as_bam)
@@ -508,7 +508,7 @@ workflow SAREK {
         }
 
         // STEP 3: Create recalibration tables
-        if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
+        if (!(params.skip_tools && params.skip_tools.contains('baserecalibrator'))) {
 
             ch_table_bqsr_no_spark = Channel.empty()
             ch_table_bqsr_spark    = Channel.empty()
@@ -589,7 +589,7 @@ workflow SAREK {
                 .map{ meta, cram, crai, table -> [ meta + [data_type: "cram"], cram, crai, table ]}
         }
 
-        if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
+        if (!(params.skip_tools && params.skip_tools.contains('baserecalibrator'))) {
             cram_variant_calling_no_spark = Channel.empty()
             cram_variant_calling_spark    = Channel.empty()
 
@@ -675,7 +675,7 @@ workflow SAREK {
         CRAM_SAMPLEQC(cram_variant_calling,
             ngscheckmate_bed,
             fasta,
-            params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'),
+            params.skip_tools && params.skip_tools.contains('baserecalibrator'),
             intervals_for_preprocessing)
 
     if (params.tools) {
@@ -766,7 +766,7 @@ workflow SAREK {
             known_sites_snps_tbi,
             known_snps_vqsr,
             params.joint_germline,
-            params.skip_tools && params.skip_tools.split(',').contains('haplotypecaller_filter'), // true if filtering should be skipped
+            params.skip_tools && params.skip_tools.contains('haplotypecaller_filter'), // true if filtering should be skipped
             params.sentieon_haplotyper_emit_mode,
             params.sentieon_dnascope_emit_mode,
             params.sentieon_dnascope_pcr_indel_model,
@@ -866,7 +866,7 @@ workflow SAREK {
         // ANNOTATE
         if (params.step == 'annotate') vcf_to_annotate = input_sample
 
-        if (params.tools.split(',').contains('merge') || params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep')|| params.tools.split(',').contains('bcfann')) {
+        if (params.tools.contains('merge') || params.tools.contains('snpeff') || params.tools.contains('vep')|| params.tools.contains('bcfann')) {
 
             vep_fasta = (params.vep_include_fasta) ? fasta : [[id: 'null'], []]
 
@@ -895,7 +895,7 @@ workflow SAREK {
     // Collate and save software versions
     //
     version_yaml = Channel.empty()
-    if (!(params.skip_tools && params.skip_tools.split(',').contains('versions'))) {
+    if (!(params.skip_tools && params.skip_tools.contains('versions'))) {
         version_yaml = softwareVersionsToYAML(versions)
             .collectFile(storeDir: "${params.outdir}/pipeline_info", name: 'nf_core_sarek_software_mqc_versions.yml', sort: true, newLine: true)
     }
@@ -903,7 +903,7 @@ workflow SAREK {
     //
     // MODULE: MultiQC
     //
-    if (!(params.skip_tools && params.skip_tools.split(',').contains('multiqc'))) {
+    if (!(params.skip_tools && params.skip_tools.contains('multiqc'))) {
 
         ch_multiqc_config                     = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
         ch_multiqc_custom_config              = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()