mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
46 lines
1.3 KiB
Text
46 lines
1.3 KiB
Text
process SALMON_INDEX {
|
|
tag "$transcript_fasta"
|
|
label "process_medium"
|
|
|
|
conda (params.enable_conda ? 'bioconda::salmon=1.5.2' : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/salmon:1.5.2--h84f40af_0' :
|
|
'quay.io/biocontainers/salmon:1.5.2--h84f40af_0' }"
|
|
|
|
input:
|
|
path genome_fasta
|
|
path transcript_fasta
|
|
|
|
output:
|
|
path "salmon" , emit: index
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
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 \\
|
|
$args \\
|
|
-i salmon
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
|
|
END_VERSIONS
|
|
"""
|
|
}
|