Fix strict syntax errors (#2159)

Fixing strict syntax errors so that I can test with Nextflow 26.04

The main change is removing if statements from config. You should be
able to just remove them without generating tons of false warnings,
since the strict syntax can validate process selectors against
conditional processes as well.

I was able to run the `test` profile with these changes on 26.03.0-edge

---------

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Famke Bäuerle <famke.baeuerle@gmail.com>

Author: bentsherman

CHANGELOG.md

@@ -50,6 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#2087](https://github.com/nf-core/sarek/pull/2087) - Move parabricks config into its own, adhere to strict syntax, swap to topics
 - [#2139](https://github.com/nf-core/sarek/pull/2139) - Back to dev (3.9.0dev)
 - [#2141](https://github.com/nf-core/sarek/pull/2141) - Update vcf_annotate_snpeff subworkflow, swap tabix/bgziptabix and snpeff to topics, strict syntax
+- [#2159](https://github.com/nf-core/sarek/pull/2159) - Fix strict syntax errors
 
 #### Fixed
 

conf/modules/aligner.config

@@ -15,7 +15,6 @@
 
 process {
 
-    if (params.step == 'mapping') {
         withName: 'BWAMEM1_MEM' {
             ext.when   = { params.aligner == 'bwa-mem' }
         }
@@ -73,8 +72,6 @@ process {
             ext.prefix = { params.split_fastq > 1 ? bam.name.replaceFirst(/\.bam$/, '_umi_extracted') : "${meta.id}_umi_extracted" }
         }
 
-    }
-
     withName: 'MERGE_BAM|INDEX_MERGE_BAM' {
         publishDir = [
             mode: params.publish_dir_mode,

conf/modules/annotate.config

@@ -16,7 +16,6 @@
 process {
 
     // SNPEFF
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
         withName: 'SNPEFF_SNPEFF' {
             ext.args   = { '-nodownload -canon -v' }
             ext.prefix = { meta.variantcaller == 'consensus' ? "${meta.id}.consensus_snpEff" : vcf.baseName - '.vcf' + '_snpEff' }
@@ -29,10 +28,8 @@ process {
                 ]
             ]
         }
-    }
 
     // VEP
-    if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
         withName: 'ENSEMBLVEP_VEP' {
             ext.args   = { ["--stats_file ",
                 meta.variantcaller == 'consensus' ? "${meta.id}.consensus_VEP.ann.summary.html" : vcf.baseName - '.vcf' + '_VEP.ann.summary.html',
@@ -62,10 +59,8 @@ process {
                 ]
             ]
         }
-    }
 
     // BCFTOOLS ANNOTATE
-    if (params.tools && params.tools.split(',').contains('bcfann')) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:BCFTOOLS_ANNOTATE' {
             ext.args   = { '--output-type z --write-index=tbi' }
             ext.prefix = { meta.variantcaller == 'consensus' ? "${meta.id}.consensus_BCF.ann" : input.baseName - '.vcf' + '_BCF.ann' }
@@ -75,7 +70,6 @@ process {
                     pattern: "*{gz,gz.tbi}"
                 ]
         }
-    }
 
     // SNPSIFT ANNOTATE
     withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:SNPSIFT_ANNMEM' {
@@ -96,7 +90,6 @@ process {
     }
 
     // SNPEFF THEN VEP
-    if (params.tools && params.tools.split(',').contains('merge')) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE' {
             ext.args   = { [
                 "--stats_file ${meta.variantcaller == 'consensus' ? "${meta.id}.consensus_snpEff_VEP.ann" : vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
@@ -114,10 +107,8 @@ process {
             // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab
             ext.prefix = { meta.variantcaller == 'consensus' ? "${meta.id}.consensus_snpEff_VEP.ann" : vcf.baseName - '.ann.vcf' + '_VEP.ann' }
         }
-    }
 
     // ALL ANNOTATION TOOLS
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge') || params.tools.split(',').contains('bcfann'))) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
             ext.prefix = { input.name - '.vcf' }
             publishDir = [
@@ -126,9 +117,7 @@ process {
                     pattern: "*{gz.tbi}"
             ]
         }
-    }
 
-    if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' {
             publishDir = [
                 mode: params.publish_dir_mode,
@@ -137,5 +126,4 @@ process {
                 saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
             ]
         }
-    }
 }

conf/modules/freebayes.config

@@ -71,7 +71,6 @@ process {
     }
 
     // PAIR_VARIANT_CALLING
-    if (params.tools && params.tools.split(',').contains('freebayes')) {
         withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
             ext.args = { "--pooled-continuous \
                             --pooled-discrete \
@@ -82,5 +81,4 @@ process {
                             --min-repeat-entropy 1 \
                             --min-alternate-count 2 " }
         }
-    }
 }

conf/modules/haplotypecaller.config

@@ -56,7 +56,6 @@ process {
         ]
     }
 
-    if (params.tools && params.tools.split(',').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 = [
@@ -66,5 +65,4 @@ process {
                 pattern: "*{bam,bai}"
             ]
         }
-    }
 }

conf/modules/joint_germline.config

@@ -32,14 +32,12 @@ 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 - ".vcf" + ".sort" }
             publishDir = [
                 enabled: false
             ]
         }
-    }
 
     withName: 'MERGE_GENOTYPEGVCFS' {
         ext.prefix = { 'joint_germline' }

conf/modules/lofreq.config

@@ -14,7 +14,6 @@
 //LOFREQ
 
 process {
-    if (params.tools && params.tools.split(',').contains('lofreq')) {
 
         withName: "LOFREQ_CALLPARALLEL" {
             ext.args = { "--call-indels" }
@@ -40,6 +39,5 @@ process {
                 pattern: "*{vcf.gz,vcf.gz.tbi}"
             ]
         }
-    }
 
 }

conf/modules/manta.config

@@ -14,7 +14,6 @@
 // MANTA
 
 process {
-    if (params.tools && params.tools.split(',').contains('manta')) {
         withName: 'MANTA_GERMLINE|MANTA_TUMORONLY|MANTA_SOMATIC' {
             ext.args   = { params.wes ? "--exome" : '' }
             ext.prefix = { "${meta.id}.manta" }
@@ -24,5 +23,4 @@ process {
                 pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}"
             ]
         }
-    }
 }

conf/modules/markduplicates.config

@@ -119,22 +119,21 @@ process {
 
     withName: 'NFCORE_SAREK:SAREK:FASTQ_PREPROCESS_GATK:CRAM_TO_BAM' {
         ext.when   = { params.save_output_as_bam }
-        if (params.tools && params.tools.split(',').contains('sentieon_dedup')) {
-            ext.prefix = { "${meta.id}.dedup" }
-            publishDir = [
+        ext.prefix = { (params.tools && params.tools.split(',').contains('sentieon_dedup'))
+            ? "${meta.id}.dedup"
+            : "${meta.id}.md" }
+        publishDir = (params.tools && params.tools.split(',').contains('sentieon_dedup'))
+            ? [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/preprocessing/sentieon_dedup/${meta.id}/" },
                 pattern: "*{dedup.bam,dedup.bam.bai}",
                 saveAs: { params.save_output_as_bam ? it : null }
             ]
-        } else {
-            ext.prefix = { "${meta.id}.md" }
-            publishDir = [
+            : [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" },
                 pattern: "*{md.bam,md.bam.bai}",
                 saveAs: { params.save_output_as_bam ? it : null }
             ]
-        }
     }
 }

conf/modules/modules.config

@@ -74,7 +74,6 @@ process {
         ]
     }
 
-    if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
         withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH' {
             ext.prefix = { "${meta.id}.recal" }
         }
@@ -88,7 +87,6 @@ process {
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
         }
-    }
 
     // VCF
     withName: 'BCFTOOLS_STATS' {