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46 lines
1.3 KiB
Text
46 lines
1.3 KiB
Text
process SALMON_INDEX {
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tag "$transcript_fasta"
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label "process_medium"
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conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' :
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'quay.io/biocontainers/salmon:1.5.2--h84f40af_0' }"
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input:
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path genome_fasta
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path transcript_fasta
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output:
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path "salmon" , emit: index
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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 get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
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def gentrome = "gentrome.fa"
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if (genome_fasta.endsWith('.gz')) {
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get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
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gentrome = "gentrome.fa.gz"
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}
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"""
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$get_decoy_ids
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sed -i.bak -e 's/>//g' decoys.txt
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cat $transcript_fasta $genome_fasta > $gentrome
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salmon \\
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index \\
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--threads $task.cpus \\
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-t $gentrome \\
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-d decoys.txt \\
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$args \\
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-i salmon
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
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END_VERSIONS
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"""
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}
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