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1 process SALMON_INDEX {
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2 tag "$meta.id"
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3 label "process_micro"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}salmon${params.fs}1.10.0" : null)
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6 conda (params.enable_conda ? 'conda-forge::libgcc-ng bioconda::salmon=1.10.1' : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_1' :
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9 'quay.io/biocontainers/salmon:1.10.1--h7e5ed60_1' }"
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10
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11 input:
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12 tuple val(meta), path(genome_fasta)
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13
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14 output:
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15 tuple val(meta), path("${meta.id}_salmon_idx"), emit: idx
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}_salmon_idx"
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24 def decoys_file = file( meta.salmon_decoys )
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25 def decoys = !("${decoys_file.simpleName}" ==~ 'dummy_file.*') && decoys_file.exits() ? "--decoys ${meta.salmon_decoys}" : ''
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26 """
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27 salmon \\
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28 index \\
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29 $decoys \\
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30 --threads $task.cpus \\
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31 $args \\
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32 --index $prefix \\
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33 --transcripts $genome_fasta
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34
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35 cat <<-END_VERSIONS > versions.yml
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36 "${task.process}":
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37 salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
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38 END_VERSIONS
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39 """
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40 } |
