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22 lines
582 B
Text
22 lines
582 B
Text
process samtools_index {
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tag "${bam.baseName}"
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container: 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
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input:
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set file(bam)
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output:
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file "*.sorted.bam"
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script:
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def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
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def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
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"""
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samtools sort $bam \\
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-@ ${task.cpus} ${avail_mem} \\
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-o ${bam.baseName}.sorted.bam
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samtools --version &> v_samtools.txt
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"""
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}
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