nf-core_modules/software/samtools/faidx/main.nf

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// Import generic module functions
include { saveFiles; getSoftwareName } from './functions'
params.options = [:]
process SAMTOOLS_FAIDX {
tag "$fasta"
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label 'process_low'
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publishDir "${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::samtools=1.10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
} else {
container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
}
input:
path fasta
output:
path "*.fai" , emit: fai
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
samtools faidx $fasta
echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
"""
}