mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 22:29:54 +00:00
49 lines
1.3 KiB
Text
49 lines
1.3 KiB
Text
|
process SAMTOOLS_INDEX {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_low'
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
|
||
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||
|
|
'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
|
||
|
|
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(input)
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.bai") , optional:true, emit: bai
|
||
|
|
tuple val(meta), path("*.csi") , optional:true, emit: csi
|
||
|
|
tuple val(meta), path("*.crai"), optional:true, emit: crai
|
||
|
|
path "versions.yml" , emit: versions
|
||
|
|
|
||
|
|
when:
|
||
|
|
task.ext.when == null || task.ext.when
|
||
|
|
|
||
|
|
script:
|
||
|
|
def args = task.ext.args ?: ''
|
||
|
|
"""
|
||
|
|
samtools \\
|
||
|
|
index \\
|
||
|
|
-@ ${task.cpus-1} \\
|
||
|
|
$args \\
|
||
|
|
$input
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
|
||
|
|
stub:
|
||
|
|
"""
|
||
|
|
touch ${input}.bai
|
||
|
|
touch ${input}.crai
|
||
|
|
touch ${input}.csi
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|