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49 lines
1.6 KiB
Plaintext
49 lines
1.6 KiB
Plaintext
process MINIMAP2_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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// Note: the versions here need to match the versions used in the mulled container below and minimap2/index
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conda "bioconda::minimap2=2.24 bioconda::samtools=1.14"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
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'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
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input:
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tuple val(meta), path(reads)
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path reference
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val bam_format
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val cigar_paf_format
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val cigar_bam
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output:
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tuple val(meta), path("*.paf"), optional: true, emit: paf
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tuple val(meta), path("*.bam"), optional: true, emit: bam
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path "versions.yml" , emit: versions
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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 args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
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def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
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"""
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minimap2 \\
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$args \\
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-t $task.cpus \\
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"${reference ?: reads}" \\
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"$reads" \\
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$cigar_paf \\
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$set_cigar_bam \\
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$bam_output
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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minimap2: \$(minimap2 --version 2>&1)
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END_VERSIONS
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"""
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}
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