33 lines
771 B
Text
33 lines
771 B
Text
process MINIMAP2 {
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tag "${prefix}"
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label 'process_medium'
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container 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0'
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input:
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tuple val(prefix), path(reads)
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path reference
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publishDir "results", mode: 'copy'
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output:
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tuple val(prefix), path("*.bam"), path("*.bam.bai")
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script:
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"""
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minimap2 \\
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-x map-ont \\
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--MD \\
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--eqx \\
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-t ${task.cpus} \\
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-a \\
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"${reference}" \\
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"${reads}" \\
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| samtools sort \\
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| samtools view \\
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-@ ${task.cpus} \\
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-b \\
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-h \\
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-o "${prefix}.bam"
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samtools index "${prefix}.bam"
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"""
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}
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