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66 lines
1.9 KiB
Text
66 lines
1.9 KiB
Text
process ARRIBA {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::arriba=2.2.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/arriba:2.2.1--hecb563c_2' :
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'quay.io/biocontainers/arriba:2.2.1--hecb563c_2' }"
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input:
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tuple val(meta), path(bam)
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path fasta
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path gtf
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path blacklist
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path known_fusions
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path structural_variants
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path tags
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path protein_domains
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output:
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tuple val(meta), path("*.fusions.tsv") , emit: fusions
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tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
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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 blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
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def known_fusions = known_fusions ? "-k $known_fusions" : ""
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def structural_variants = structural_variants ? "-d $structual_variants" : ""
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def tags = tags ? "-t $tags" : ""
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def protein_domains = protein_domains ? "-p $protein_domains" : ""
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"""
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arriba \\
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-x $bam \\
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-a $fasta \\
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-g $gtf \\
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-o ${prefix}.fusions.tsv \\
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-O ${prefix}.fusions.discarded.tsv \\
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$blacklist \\
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$known_fusions \\
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$structural_variants \\
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$tags \\
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$protein_domains \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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arriba: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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echo stub > ${prefix}.fusions.tsv
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echo stub > ${prefix}.fusions.discarded.tsv
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echo "${task.process}:" > versions.yml
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echo ' arriba: 2.2.1' >> versions.yml
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"""
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}
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