mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-24 11:48:17 +00:00
51 lines
1.6 KiB
Text
51 lines
1.6 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
def options = initOptions(params.options)
|
|
|
|
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:getSoftwareName(task.process), publish_id:'') }
|
|
|
|
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"
|
|
}
|
|
|
|
input:
|
|
path genome_fasta
|
|
path transcript_fasta
|
|
|
|
output:
|
|
path "salmon" , emit: index
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
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"
|
|
}
|
|
"""
|
|
$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
|
|
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
|
|
"""
|
|
}
|