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adding explicit temps #541

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merged 2 commits into from
Apr 29, 2024
Merged

adding explicit temps #541

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8e02814
adding explicit temps
jemten Apr 29, 2024
b2ee216
adds trailing comma
jemten Apr 29, 2024
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2 changes: 2 additions & 0 deletions conf/modules/align_bwa_bwamem2.config
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Original file line number Diff line number Diff line change
Expand Up @@ -19,12 +19,14 @@ process {

withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWAMEM2_MEM' {
ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
ext.args2 = { "-T ./samtools_sort_tmp" }
ext.prefix = { "${meta.id}_sorted" }
ext.when = { params.aligner.equals("bwamem2") }
}

withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:BWA_MEM' {
ext.args = { "-M -K 100000000 -R ${meta.read_group}" }
ext.args2 = { "-T ./samtools_sort_tmp" }
ext.prefix = { "${meta.id}_sorted" }
ext.when = { params.aligner.equals("bwa") }
}
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7 changes: 6 additions & 1 deletion conf/modules/prepare_references.config
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Expand Up @@ -115,7 +115,12 @@ process {
}

withName: '.*PREPARE_REFERENCES:GATK_PREPROCESS_WGS' {
ext.args = { "--padding 0 --interval-merging-rule OVERLAPPING_ONLY --exclude-intervals ${params.mito_name}" }
ext.args = { [
'--padding 0',
'--interval-merging-rule OVERLAPPING_ONLY',
"--exclude-intervals ${params.mito_name}",
"--temp-dir ./"
].join(' ') }
ext.when = { params.analysis_type.equals("wgs") && !params.readcount_intervals }
}

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24 changes: 15 additions & 9 deletions conf/modules/rank_variants.config
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Expand Up @@ -21,22 +21,24 @@ process {
ext.prefix = { "${meta.id}_sv_genmod_annotate_${meta.set}" }
ext.args = { [
'--annotate_regions',
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38',
'--temp_dir ./'
].join(' ') }
}

withName: '.*RANK_VARIANTS_SV:GENMOD_MODELS' {
ext.prefix = { "${meta.id}_sv_genmod_models_${meta.set}" }
ext.args = " --whole_gene "
ext.args = "--whole_gene --temp_dir ./"
}

withName: '.*RANK_VARIANTS_SV:GENMOD_SCORE' {
ext.prefix = { "${meta.id}_sv_genmod_score_${meta.set}" }
ext.args = " --rank_results "
ext.args = "--rank_results"
}

withName: '.*RANK_VARIANTS_SV:GENMOD_COMPOUND' {
ext.prefix = { "${meta.id}_sv_genmod_compound_${meta.set}" }
ext.args = "--temp_dir ./"
}

withName: '.*RANK_VARIANTS_SV:BCFTOOLS_SORT' {
Expand Down Expand Up @@ -72,22 +74,24 @@ process {
ext.prefix = { "${meta.id}_snv_genmod_annotate_${meta.set}" }
ext.args = { [
'--annotate_regions',
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38',
'--temp_dir ./'
].join(' ') }
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_MODELS' {
ext.prefix = { "${meta.id}_snv_genmod_models_${meta.set}" }
ext.args = " --whole_gene "
ext.args = "--whole_gene --temp_dir ./"
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_SCORE' {
ext.prefix = { "${meta.id}_snv_genmod_score_${meta.set}" }
ext.args = " --rank_results "
ext.args = "--rank_results"
}

withName: '.*RANK_VARIANTS_SNV:GENMOD_COMPOUND' {
ext.prefix = { "${meta.id}_snv_genmod_compound_${meta.set}" }
ext.args = "--temp_dir ./"
}

withName: '.*RANK_VARIANTS_SNV:BCFTOOLS_SORT' {
Expand Down Expand Up @@ -122,22 +126,24 @@ process {
ext.prefix = { "${meta.id}_mt_genmod_annotate_${meta.set}" }
ext.args = { [
'--annotate_regions',
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38'
params.genome.equals('GRCh37') ? '--genome-build 37' : '--genome-build 38',
'--temp_dir ./'
].join(' ') }
}

withName: '.*RANK_VARIANTS_MT:GENMOD_MODELS' {
ext.prefix = { "${meta.id}_mt_genmod_models_${meta.set}" }
ext.args = " --whole_gene "
ext.args = "--whole_gene --temp_dir ./"
}

withName: '.*RANK_VARIANTS_MT:GENMOD_SCORE' {
ext.prefix = { "${meta.id}_mt_genmod_score_${meta.set}" }
ext.args = " --rank_results "
ext.args = "--rank_results"
}

withName: '.*RANK_VARIANTS_MT:GENMOD_COMPOUND' {
ext.prefix = { "${meta.id}_mt_genmod_compound_${meta.set}" }
ext.args = "--temp_dir ./"
}

withName: '.*RANK_VARIANTS_MT:BCFTOOLS_SORT' {
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2 changes: 1 addition & 1 deletion conf/modules/raredisease.config
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ process {
process {

withName: '.*RAREDISEASE:FASTQC' {
ext.args = '--quiet'
ext.args = '--quiet --dir ./'
publishDir = [
path: { "${params.outdir}/fastqc/${meta.id}" },
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
Expand Down
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