nf-core_modules/modules/samtools/faidx/main.nf
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SAMTOOLS_FAIDX {
tag "$fasta"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
} else {
container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
}
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
"""
}