[WIP] --tools is now case insensitive

CHANGELOG.md

@@ -20,6 +20,7 @@ Rapaselet is a delta formed by the Rapaätno river between the Bielloriehppe mas
 - [#1173](https://github.com/nf-core/sarek/pull/1173) - CI tests for VQSR track with stub runs
 - [#1122](https://github.com/nf-core/sarek/pull/1122), [#1196](https://github.com/nf-core/sarek/pull/1196) - Add `annotation cache` functionality
 - [#1184](https://github.com/nf-core/sarek/pull/1184) - Stub-based CI-test of Sentieon joint-germline variant-calling with VQSR
+- [#1188](https://github.com/nf-core/sarek/pull/1188) - `--tools` is now case insensitive
 
 ### Changed
 

checkInParam.nf

@@ -0,0 +1,21 @@
+
+// Global function
+// Check the parameters tools or skip_tools, then compare it against the provided tool
+// Returns true/false based on whether 'tool' is found in 'parameter'
+def checkInParam(parameter, checkValue) {
+    if (!parameter){
+        false
+    } else {
+        def tokenized_parameter = parameter.tokenize(',')
+        switch (checkValue) {
+            // If checkValue is a list check if any appear in tokenized parameter
+            case checkValue instanceof List:
+                checkValue.any{ it.toLowerCase() in parameter.tokenize(',') }
+            // If checkValue is a string check it appears in parameter
+            case checkValue instanceof String:
+                checkValue.toLowerCase() in parameter.tokenize(',')
+            default:
+                false
+        }
+    }
+}

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'))
+                            (checkInParam(params.skip_tools, 'markduplicates')) &&
+                            !(checkInParam(params.tools, '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 && !checkInParam(params.skip_tools, '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}/${it}" : null }
+            saveAs: { (params.save_output_as_bam && (params.save_mapped || checkInParam(params.skip_tools, 'markduplicates'))) ? "mapped/${meta.id}/${it}" : null }
         ]
     }
 

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 && (checkInParam(params.tools, 'snpeff') || checkInParam(params.tools, 'merge'))) {
         withName: 'SNPEFF_SNPEFF' {
             ext.prefix       = { vcf.baseName - ".vcf" + "_snpEff" }
             ext.args         = '-nodownload -canon -v'
@@ -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: { checkInParam(params.tools, 'snpeff') ? it : null }
                 ]
             ]
         }
     }
 
     // VEP
-    if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
+    if (params.tools && (checkInParam(params.tools, 'vep') || checkInParam(params.tools, 'merge'))) {
         withName: 'ENSEMBLVEP_VEP' {
             ext.args         = { [
                 (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
@@ -61,15 +61,15 @@ process {
     }
 
     // SNPEFF THEN VEP
-    if (params.tools && params.tools.split(',').contains('merge')) {
+    if (checkInParam(params.tools, '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 - ".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'))) {
+    if (params.tools && (checkInParam(params.tools, 'snpeff') || checkInParam(params.tools, 'vep') || checkInParam(params.tools, 'merge'))) {
         withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)" {
             ext.prefix       = { input.name - ".vcf" }
             publishDir       = [
@@ -80,13 +80,13 @@ process {
         }
     }
 
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
+    if (params.tools && (checkInParam(params.tools, 'snpeff') || checkInParam(params.tools, '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: { checkInParam(params.tools, 'snpeff') ? it : null }
             ]
         }
     }

conf/modules/ascat.config

@@ -26,7 +26,7 @@ process {
             "min_base_qual": params.ascat_min_base_qual,
             "min_map_qual": params.ascat_min_map_qual
             ]}
-        ext.when         = { params.tools && params.tools.split(',').contains('ascat') }
+        ext.when         = { checkInParam(params.tools, 'ascat') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/ascat/${meta.id}/" },

conf/modules/cnvkit.config

@@ -17,7 +17,7 @@ process {
 
 // PREPARE REFERENCE CNVKIT
     withName: 'CNVKIT_ANTITARGET' {
-        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') }
+        ext.when         = { checkInParam(params.tools, 'cnvkit') }
         publishDir       = [
             enabled: params.save_reference,
             mode: params.publish_dir_mode,
@@ -28,7 +28,7 @@ process {
 
     withName: 'CNVKIT_REFERENCE' {
         ext.prefix       = "cnvkit"
-        ext.when         = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
+        ext.when         = { checkInParam(params.tools, 'cnvkit') && !params.cnvkit_reference }
         publishDir       = [
             enabled: params.save_reference,
             mode: params.publish_dir_mode,
@@ -40,7 +40,7 @@ process {
     // CNVKIT
     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         = { checkInParam(params.tools, 'cnvkit') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" },

conf/modules/controlfreec.config

@@ -24,7 +24,7 @@ process {
     }
 
     withName: 'FREEC_.*' {
-        ext.when         = { params.tools && params.tools.split(',').contains('controlfreec') }
+        ext.when         = { checkInParam(params.tools, 'controlfreec') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" },

conf/modules/deepvariant.config

@@ -18,7 +18,7 @@ process {
     withName: 'DEEPVARIANT' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" }
         ext.args         = { params.wes ?  "--model_type WES" : "--model_type WGS" }
-        ext.when         = { params.tools && params.tools.split(',').contains('deepvariant') }
+        ext.when         = { checkInParam(params.tools, 'deepvariant') }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },

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.simpleName}" }
-        ext.when         = { params.tools && params.tools.split(',').contains('freebayes') }
+        ext.when         = { checkInParam(params.tools, 'freebayes') }
         publishDir       = [
             enabled: false
         ]
@@ -53,7 +53,7 @@ process {
     }
 
     // PAIR_VARIANT_CALLING
-    if (params.tools && params.tools.split(',').contains('freebayes')) {
+    if (checkInParam(params.tools, 'freebayes')) {
         withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
             ext.args       = "--pooled-continuous \
                             --pooled-discrete \

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.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
-        ext.when         = { params.tools && params.tools.split(',').contains('haplotypecaller') }
+        ext.when         = { checkInParam(params.tools, '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 (checkInParam(params.tools, '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       = [

conf/modules/joint_germline.config

@@ -30,7 +30,7 @@ process {
         ]
     }
 
-    if (params.tools && params.tools.contains('haplotypecaller') && params.joint_germline) {
+    if (checkInParam(params.tools, 'haplotypecaller') && params.joint_germline) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_JOINT_CALLING_GERMLINE_GATK:BCFTOOLS_SORT' {
             ext.prefix       = { vcf.baseName - ".vcf" + ".sort" }
             publishDir       = [

conf/modules/manta.config

@@ -14,7 +14,7 @@
 // MANTA
 
 process {
-    if (params.tools && params.tools.split(',').contains('manta')) {
+    if (checkInParam(params.tools, 'manta')) {
         withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
             ext.args         = { params.wes ? "--exome" : "" }
             ext.prefix       = { "${meta.id}.manta" }

conf/modules/markduplicates.config

@@ -34,7 +34,7 @@ process {
     }
 
     withName: 'NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' {
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'samtools')) }
         ext.prefix       = { "${meta.id}.md.cram" }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -47,8 +47,8 @@ process {
         // Run only when mapping should be saved as CRAM or when no MD is done
         ext.when         = (params.save_mapped && !params.save_output_as_bam) ||
             (
-                (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
-                !(params.tools && params.tools.split(',').contains('sentieon_dedup'))
+                (checkInParam(params.skip_tools, 'markduplicates')) &&
+                !(checkInParam(params.tools, 'sentieon_dedup'))
             )
         ext.prefix       = { "${meta.id}.sorted" }
         publishDir       = [
@@ -62,7 +62,7 @@ process {
 
     withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' {
         ext.prefix       = { "${meta.id}.md.cram" }
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'markduplicates_report')) }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${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         = { !(checkInParam(params.skip_tools, 'markduplicates')) }
         publishDir       = [
             [
                 enabled: !params.save_output_as_bam,
@@ -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}/${it}" : null}
+                saveAs: { !(checkInParam(params.skip_tools, 'markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null}
             ]
         ]
     }
@@ -112,7 +112,7 @@ 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 (checkInParam(params.tools, 'sentieon_dedup')) {
             ext.prefix       = { "${meta.id}.dedup" }
             publishDir       = [
                 enabled: params.save_output_as_bam,

conf/modules/modules.config

@@ -30,7 +30,7 @@ process {
 // QC
     withName: 'FASTQC' {
         ext.args         = '--quiet'
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'fastqc')) }
         publishDir       = [
             [
                 path: { "${params.outdir}/reports/fastqc/${meta.id}" },
@@ -41,7 +41,7 @@ process {
     }
 
     withName: 'NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS' {
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'samtools')) }
         ext.prefix       = { "${meta.id}.sorted.cram" }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -53,30 +53,30 @@ process {
     withName: 'MOSDEPTH' {
         ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""}
         ext.prefix       = {
-            if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
+            if (checkInParam(params.tools, 'sentieon_dedup')) {
                 "${meta.id}.dedup"
-            } else if (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) {
+            } else if (checkInParam(params.skip_tools, 'markduplicates')) {
                 "${meta.id}.sorted"
             } else {
                 "${meta.id}.md"
             }
         }
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'mosdepth')) }
         publishDir = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/reports/mosdepth/${meta.id}" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
-    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') && (!(checkInParam(params.skip_tools, 'baserecalibrator')))) {
         withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH' {
             ext.prefix       = { "${meta.id}.recal" }
         }
 
         withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS' {
             ext.prefix       = { "${meta.id}.recal.cram" }
-            ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
+            ext.when         = { !(checkInParam(params.skip_tools, 'samtools')) }
             publishDir       = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/reports/samtools/${meta.id}" },
@@ -87,7 +87,7 @@ process {
 
     // VCF
     withName: 'BCFTOOLS_STATS' {
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('bcftools')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'bcftools')) }
         ext.prefix       = { vcf.baseName - ".vcf" }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -97,7 +97,7 @@ process {
     }
 
     withName: 'VCFTOOLS_.*' {
-        ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('vcftools')) }
+        ext.when         = { !(checkInParam(params.skip_tools, 'vcftools')) }
         ext.prefix       = { variant_file.baseName - ".vcf" }
         publishDir       = [
             mode: params.publish_dir_mode,

conf/modules/mpileup.config

@@ -23,7 +23,7 @@ process {
 
     withName: 'BCFTOOLS_MPILEUP' {
         ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.bcftools" : "${meta.id}_${intervals.simpleName}.bcftools" }
-        ext.when   = { params.tools && params.tools.split(',').contains('mpileup') }
+        ext.when   = { checkInParam(params.tools, 'mpileup') }
         ext.args2  = "--multiallelic-caller"
         ext.args3  = "-i 'count(GT==\"RR\")==0'" // only report non homozygous reference variants
         publishDir = [
@@ -44,15 +44,15 @@ process {
     }
 
     withName: 'SAMTOOLS_MPILEUP' {
-        ext.when   = { params.tools && params.tools.split(',').contains('controlfreec') }
+        ext.when   = { checkInParam(params.tools, 'controlfreec') }
         publishDir = [
             enabled: false
         ]
 
     }
 
 // PAIR_VARIANT_CALLING
-    if (params.tools && params.tools.split(',').contains('controlfreec')) {
+    if (checkInParam(params.tools, '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" }
         }