31 lines
674 B
Text
31 lines
674 B
Text
process QUASIRECOMB {
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tag "${prefix}"
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label 'process_high'
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label 'quasirecomb'
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container 'quay.io/biocontainers/quasirecomb:1.2--hdfd78af_1'
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input:
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tuple val(prefix), path(bam), path(bai)
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output:
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tuple val(prefix), path("*.fasta")
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publishDir "${params.outdir}/${task.process}", mode: 'copy'
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when:
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task.ext.when == null || task.ext.when
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script:
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def jmemstring = task.memory.toMega() + 'M'
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"""
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quasirecomb \\
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-XX:+UseParallelGC \\
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-Xms2g \\
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-Xmx${jmemstring} \\
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-XX:+UseNUMA \\
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-XX:NewRatio=9 \\
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-i "${bam}"
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mv quasispecies.fasta "${prefix}.fasta"
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"""
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}
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