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37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process SALMON_INDEX {
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tag "$fasta"
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label "process_medium"
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
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//container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
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conda (params.conda ? "bioconda::salmon=1.3.0" : null)
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input:
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path fasta
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val options
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output:
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path "salmon" , emit: index
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path "*.version.txt", emit: version
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script:
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def software = getSoftwareName(task.process)
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def ioptions = initOptions(options)
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"""
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salmon \\
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index \\
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--threads $task.cpus \\
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-t $fasta \\
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$ioptions.args \\
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-i salmon
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salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
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"""
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}
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