nf-core_modules/software/salmon/index/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
def options = initOptions(params.options)
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process SALMON_INDEX {
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tag "$transcript_fasta"
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label "process_medium"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
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conda (params.enable_conda ? "bioconda::salmon=1.4.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/salmon:1.4.0--hf69c8f4_0"
} else {
container "quay.io/biocontainers/salmon:1.4.0--hf69c8f4_0"
}
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input:
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path genome_fasta
path transcript_fasta
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output:
path "salmon" , emit: index
path "*.version.txt", emit: version
script:
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def software = getSoftwareName(task.process)
def get_decoy_ids = "grep '^>' $genome_fasta | cut -d ' ' -f 1 > decoys.txt"
def gentrome = "gentrome.fa"
if (genome_fasta.endsWith('.gz')) {
get_decoy_ids = "grep '^>' <(gunzip -c $genome_fasta) | cut -d ' ' -f 1 > decoys.txt"
gentrome = "gentrome.fa.gz"
}
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"""
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$get_decoy_ids
sed -i.bak -e 's/>//g' decoys.txt
cat $transcript_fasta $genome_fasta > $gentrome
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salmon \\
index \\
--threads $task.cpus \\
-t $gentrome \\
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-d decoys.txt \\
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$options.args \\
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-i salmon
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
"""
}