mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
|
// Import generic module functions
|
||
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
||
|
|
|
||
|
|
process SALMON_INDEX {
|
||
|
|
tag "$fasta"
|
||
|
|
label "process_medium"
|
||
|
|
publishDir "${params.outdir}",
|
||
|
|
mode: params.publish_dir_mode,
|
||
|
|
saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:'') }
|
||
|
|
|
||
|
|
container "quay.io/biocontainers/salmon:1.3.0--hf69c8f4_0"
|
||
|
|
//container "https://depot.galaxyproject.org/singularity/salmon:1.3.0--hf69c8f4_0"
|
||
|
|
|
||
|
|
conda (params.conda ? "bioconda::salmon=1.3.0" : null)
|
||
|
|
|
||
|
|
input:
|
||
|
|
path fasta
|
||
|
|
val options
|
||
|
|
|
||
|
|
output:
|
||
|
|
path "salmon" , emit: index
|
||
|
|
path "*.version.txt", emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def software = getSoftwareName(task.process)
|
||
|
|
def ioptions = initOptions(options)
|
||
|
|
"""
|
||
|
|
salmon \\
|
||
|
|
index \\
|
||
|
|
--threads $task.cpus \\
|
||
|
|
-t $fasta \\
|
||
|
|
$ioptions.args \\
|
||
|
|
-i salmon
|
||
|
|
salmon --version | sed -e "s/salmon //g" > ${software}.version.txt
|
||
|
|
"""
|
||
|
|
}
|