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remove cpu restrictions (#760)
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Ramprasad Neethiraj
GitHub
parent
22ec5c6007
commit
216dc8c984
5 changed files with 12 additions and 17 deletions
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@ -29,7 +29,6 @@ process BOWTIE_ALIGN {
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tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
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script:
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def split_cpus = Math.floor(task.cpus/2)
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
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@ -37,7 +36,7 @@ process BOWTIE_ALIGN {
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"""
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INDEX=`find -L ./ -name "*.3.ebwt" | sed 's/.3.ebwt//'`
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bowtie \\
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--threads ${split_cpus} \\
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--threads $task.cpus \\
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--sam \\
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-x \$INDEX \\
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-q \\
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@ -45,7 +44,7 @@ process BOWTIE_ALIGN {
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$options.args \\
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$endedness \\
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2> ${prefix}.out \\
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| samtools view $options.args2 -@ ${split_cpus} -bS -o ${prefix}.bam -
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| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
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if [ -f ${prefix}.unmapped.fastq ]; then
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gzip ${prefix}.unmapped.fastq
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@ -29,7 +29,6 @@ process BOWTIE2_ALIGN {
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tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
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script:
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def split_cpus = Math.floor(task.cpus/2)
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (meta.single_end) {
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@ -39,11 +38,11 @@ process BOWTIE2_ALIGN {
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bowtie2 \\
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-x \$INDEX \\
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-U $reads \\
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--threads $split_cpus \\
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--threads $task.cpus \\
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$unaligned \\
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$options.args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ ${split_cpus} $options.args2 -bhS -o ${prefix}.bam -
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| samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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@ -60,11 +59,11 @@ process BOWTIE2_ALIGN {
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-x \$INDEX \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--threads $split_cpus \\
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--threads $task.cpus \\
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$unaligned \\
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$options.args \\
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2> ${prefix}.bowtie2.log \\
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| samtools view -@ ${split_cpus} $options.args2 -bhS -o ${prefix}.bam -
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| samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
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if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
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mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
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@ -27,7 +27,6 @@ process BWA_MEM {
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path "versions.yml" , emit: version
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script:
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def split_cpus = Math.floor(task.cpus/2)
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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@ -37,10 +36,10 @@ process BWA_MEM {
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bwa mem \\
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$options.args \\
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$read_group \\
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-t $split_cpus \\
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-t $task.cpus \\
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\$INDEX \\
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$reads \\
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| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
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| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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@ -27,7 +27,6 @@ process BWAMEM2_MEM {
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path "versions.yml" , emit: version
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script:
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def split_cpus = Math.floor(task.cpus/2)
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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@ -38,10 +37,10 @@ process BWAMEM2_MEM {
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mem \\
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$options.args \\
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$read_group \\
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-t $split_cpus \\
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-t $task.cpus \\
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\$INDEX \\
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$reads \\
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| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
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| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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@ -27,7 +27,6 @@ process BWAMETH_ALIGN {
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path "versions.yml" , emit: version
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script:
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def split_cpus = Math.floor(task.cpus/2)
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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@ -37,10 +36,10 @@ process BWAMETH_ALIGN {
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bwameth.py \\
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$options.args \\
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$read_group \\
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-t ${split_cpus} \\
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-t $task.cpus \\
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--reference \$INDEX \\
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$reads \\
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| samtools view $options.args2 -@ ${split_cpus} -bhS -o ${prefix}.bam -
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| samtools view $options.args2 -@ $task.cpus -bhS -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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