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

38 lines
1.3 KiB
Text
Raw Normal View History

2020-12-17 23:50:24 +00:00
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
2020-12-17 23:50:24 +00:00
params.options = [:]
options = initOptions(params.options)
2020-12-17 23:50:24 +00:00
process SAMTOOLS_INDEX {
tag "$meta.id"
label 'process_low'
2020-12-17 23:50:24 +00:00
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
2020-12-17 23:50:24 +00:00
conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
2020-12-17 23:50:24 +00:00
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
2020-12-17 23:50:24 +00:00
} else {
container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
2020-12-17 23:50:24 +00:00
}
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.bai"), optional:true, emit: bai
tuple val(meta), path("*.csi"), optional:true, emit: csi
path "versions.yml" , emit: versions
2020-12-17 23:50:24 +00:00
script:
"""
samtools index $options.args $bam
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
2020-12-17 23:50:24 +00:00
"""
}