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38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::metabat2=2.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/metabat2:2.15--h986a166_1' :
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'quay.io/biocontainers/metabat2:2.15--h986a166_1' }"
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("*.txt.gz"), emit: depth
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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 ?: "${meta.id}"
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"""
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export OMP_NUM_THREADS=$task.cpus
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jgi_summarize_bam_contig_depths \\
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--outputDepth ${prefix}.txt \\
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$args \\
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$bam
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bgzip --threads $task.cpus ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' )
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END_VERSIONS
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"""
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}
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