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

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process SALMON_INDEX {
tag "$transcript_fasta"
label "process_medium"
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'index', meta:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0"
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} else {
container "quay.io/biocontainers/salmon:1.5.2--h84f40af_0"
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}
input:
path genome_fasta
path transcript_fasta
output:
path "salmon" , emit: index
path "versions.yml" , emit: versions
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script:
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"
}
"""
$get_decoy_ids
sed -i.bak -e 's/>//g' decoys.txt
cat $transcript_fasta $genome_fasta > $gentrome
salmon \\
index \\
--threads $task.cpus \\
-t $gentrome \\
-d decoys.txt \\
$options.args \\
-i salmon
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
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"""
}