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Refactor to adhere to language server #1912

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318f05a
update subworkflows to adhere to lang server
FriederikeHanssen May 30, 2025
ab61b4e
fix trace suffix param
FriederikeHanssen May 30, 2025
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93 changes: 46 additions & 47 deletions conf/modules/aligner.config
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Original file line number Diff line number Diff line change
Expand Up @@ -15,61 +15,60 @@

process {

if (params.step == 'mapping') {
withName: 'BWAMEM1_MEM' {
ext.when = { params.aligner == 'bwa-mem' }
}
withName: "BWAMEM1_MEM" {
ext.when = { params.aligner == 'bwa-mem' }
}

withName: 'BWAMEM2_MEM' {
ext.when = { params.aligner == 'bwa-mem2' }
}
withName: 'BWAMEM2_MEM' {
ext.when = { params.aligner == 'bwa-mem2' }
}

withName: 'DRAGMAP_ALIGN' {
ext.args = { "--RGSM ${meta.patient}_${meta.sample} --RGID ${meta.read_group}" }
ext.when = { params.aligner == 'dragmap' }
}
withName: 'DRAGMAP_ALIGN' {
ext.args = { "--RGSM ${meta.patient}_${meta.sample} --RGID ${meta.read_group}" }
ext.when = { params.aligner == 'dragmap' }
}

withName: 'SENTIEON_BWAMEM' {
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]).concat('.bam') : "${meta.id}.sorted.bam" }
ext.when = { params.aligner == 'sentieon-bwamem' }
}
withName: 'SENTIEON_BWAMEM' {
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]).concat('.bam') : "${meta.id}.sorted.bam" }
ext.when = { params.aligner == 'sentieon-bwamem' }
}

withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*bam",
// Only save if save_output_as_bam AND
// (save_mapped OR no_markduplicates OR sentieon_dedup) AND
// only a single BAM file per sample
saveAs: {
if (params.save_output_as_bam &&
(
params.save_mapped ||
(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
!(params.tools && params.tools.split(',').contains('sentieon_dedup'))
) && (meta.size * meta.num_lanes == 1)
) { "mapped/${meta.id}/${it}" }
else { null }
}
]
}
withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/" },
pattern: "*bam",
// Only save if save_output_as_bam AND
// (save_mapped OR no_markduplicates OR sentieon_dedup) AND
// only a single BAM file per sample
saveAs: {
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'))
) && (meta.size * meta.num_lanes == 1)
) { "mapped/${meta.id}/${it}" }
else { null }
}
]
}

withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN' {
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
// 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' : '' }
}
withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN' {
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
// 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' : '' }
}

withName: 'BWAMEM.*_MEM|SENTIEON_BWAMEM' {
// Using -B 3 for tumor samples
ext.args = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" }
}
withName: 'BWAMEM.*_MEM|SENTIEON_BWAMEM' {
// Using -B 3 for tumor samples
ext.args = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" }
}


withName: 'MERGE_BAM|INDEX_MERGE_BAM' {
publishDir = [
mode: params.publish_dir_mode,
Expand Down
151 changes: 70 additions & 81 deletions conf/modules/annotate.config
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Original file line number Diff line number Diff line change
Expand Up @@ -16,102 +16,91 @@
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 = { vcf.baseName - '.vcf' + '_snpEff' }
publishDir = [
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
pattern: "*{csv,html,genes.txt}",
saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
]
withName: 'SNPEFF_SNPEFF' {
ext.args = { '-nodownload -canon -v' }
ext.prefix = { vcf.baseName - '.vcf' + '_snpEff' }
publishDir = [
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" },
pattern: "*{csv,html,genes.txt}",
saveAs: { params.tools.split(',').contains('snpeff') ? it : null }
]
}
]
}


// VEP
if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
withName: 'ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
(params.vep_custom_args) ?: ''
].join(' ').trim() }
// If just VEP: <vcf prefix>_VEP.ann.vcf
ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' }
publishDir = [
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" },
pattern: "*html"
],
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz}"
]
withName: 'ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.vcf' + '_VEP.ann'}.summary.html",
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
(params.vep_custom_args) ?: ''
].join(' ').trim() }
// If just VEP: <vcf prefix>_VEP.ann.vcf
ext.prefix = { vcf.baseName - '.vcf' + '_VEP.ann' }
publishDir = [
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" },
pattern: "*html"
],
[
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz}"
]
}
]
}

// BCFTOOLS ANNOTATE
if (params.tools && params.tools.split(',').contains('bcfann')) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
ext.args = { '--output-type z --write-index=tbi' }
ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz,gz.tbi}"
]
}
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
ext.args = { '--output-type z --write-index=tbi' }
ext.prefix = { input.baseName - '.vcf' + '_BCF.ann' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
pattern: "*{gz,gz.tbi}"
]
}

// SNPEFF THEN VEP
if (params.tools && params.tools.split(',').contains('merge')) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
(params.vep_custom_args) ?: ''
].join(' ').trim() }
// 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' }
}
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP_VEP' {
ext.args = { [
"--stats_file ${vcf.baseName - '.ann.vcf' + '_VEP.ann'}.summary.html",
(params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '',
(params.vep_loftee) ? "--plugin LoF,loftee_path:/usr/local/share/ensembl-vep-${params.vep_version}" : '',
(params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '',
(params.vep_spliceregion) ? '--plugin SpliceRegion' : '',
(params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf',
(params.vep_custom_args) ?: ''
].join(' ').trim() }
// 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') || params.tools.split(',').contains('bcfann'))) {
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
ext.prefix = { input.name - '.vcf' }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },
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 = [
withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:(TABIX_BGZIPTABIX|TABIX_TABIX)' {
ext.prefix = { input.name - '.vcf' }
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 }
]
}
pattern: "*{gz.tbi}"
]
}

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 }
]
}
}
20 changes: 9 additions & 11 deletions conf/modules/freebayes.config
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Original file line number Diff line number Diff line change
Expand Up @@ -53,16 +53,14 @@ 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 \
--genotype-qualities \
--report-genotype-likelihood-max \
--allele-balance-priors-off \
--min-alternate-fraction 0.03 \
--min-repeat-entropy 1 \
--min-alternate-count 2 " }
}
withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
ext.args = { "--pooled-continuous \
--pooled-discrete \
--genotype-qualities \
--report-genotype-likelihood-max \
--allele-balance-priors-off \
--min-alternate-fraction 0.03 \
--min-repeat-entropy 1 \
--min-alternate-count 2 " }
}
}
18 changes: 8 additions & 10 deletions conf/modules/haplotypecaller.config
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Original file line number Diff line number Diff line change
Expand Up @@ -56,15 +56,13 @@ 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 = { "${meta.id}.realigned" }
publishDir = [
enabled: true,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" },
pattern: "*{bam,bai}"
]
}
withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' {
ext.prefix = { "${meta.id}.realigned" }
publishDir = [
enabled: true,
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" },
pattern: "*{bam,bai}"
]
}
}
19 changes: 8 additions & 11 deletions conf/modules/indexcov.config
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Original file line number Diff line number Diff line change
Expand Up @@ -2,19 +2,16 @@
// INDEXCOV

process {
if (params.tools && params.tools.split(',').contains('indexcov')) {

withName: 'SAMTOOLS_REINDEX_BAM' {
ext.args = { ' -F 3844 -q 30 ' } // high mapq , primary read paired properly mapped
}

withName: 'GOLEFT_INDEXCOV' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/indexcov/" }
]
withName: 'SAMTOOLS_REINDEX_BAM' {
ext.args = { ' -F 3844 -q 30 ' } // high mapq , primary read paired properly mapped
}

}
withName: 'GOLEFT_INDEXCOV' {
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/indexcov/" }
]

}

Expand Down
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