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46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
process MAXBIN2 {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::maxbin2=2.2.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/maxbin2:2.2.7--he1b5a44_2' :
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'quay.io/biocontainers/maxbin2:2.2.7--he1b5a44_2' }"
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input:
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tuple val(meta), path(contigs), path(reads), path(abund)
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output:
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tuple val(meta), path("*.fasta.gz") , emit: binned_fastas
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tuple val(meta), path("*.summary") , emit: summary
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tuple val(meta), path("*.log.gz") , emit: log
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tuple val(meta), path("*.marker.gz") , emit: marker_counts
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tuple val(meta), path("*.noclass.gz") , emit: unbinned_fasta
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tuple val(meta), path("*.tooshort.gz"), emit: tooshort_fasta
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tuple val(meta), path("*_bin.tar.gz") , emit: marker_bins , optional: true
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tuple val(meta), path("*_gene.tar.gz"), emit: marker_genes, optional: true
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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 associate_files = reads ? "-reads $reads" : "-abund $abund"
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"""
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run_MaxBin.pl \\
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-contig $contigs \\
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$associate_files \\
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-thread $task.cpus \\
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$args \\
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-out $prefix
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gzip *.fasta *.noclass *.tooshort *log *.marker
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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maxbin2: \$( run_MaxBin.pl -v | head -n 1 | sed 's/MaxBin //' )
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END_VERSIONS
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"""
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}
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