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45 lines
1.9 KiB
Text
45 lines
1.9 KiB
Text
process ISOSEQ3_CLUSTER {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' :
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'quay.io/biocontainers/isoseq3:3.4.0--0' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.transcripts.bam") , emit: bam
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tuple val(meta), path("*.transcripts.bam.pbi") , emit: pbi
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tuple val(meta), path("*.transcripts.cluster") , emit: cluster
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tuple val(meta), path("*.transcripts.cluster_report.csv"), emit: cluster_report
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tuple val(meta), path("*.transcripts.transcriptset.xml") , emit: transcriptset
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tuple val(meta), path("*.transcripts.hq.bam") , optional: true, emit: hq_bam
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tuple val(meta), path("*.transcripts.hq.bam.pbi") , optional: true, emit: hq_pbi
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tuple val(meta), path("*.transcripts.lq.bam") , optional: true, emit: lq_bam
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tuple val(meta), path("*.transcripts.lq.bam.pbi") , optional: true, emit: lq_pbi
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tuple val(meta), path("*.transcripts.singletons.bam") , optional: true, emit: singletons_bam
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tuple val(meta), path("*.transcripts.singletons.bam.pbi"), optional: true, emit: singletons_pbi
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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 ?: "${meta.id}"
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"""
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isoseq3 \\
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cluster \\
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$bam \\
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${prefix}.transcripts.bam \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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isoseq3: \$( isoseq3 cluster --version|sed 's/isoseq cluster //g'|sed 's/ (.*//g' )
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END_VERSIONS
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"""
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}
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