nf-core_modules/modules/snpsites/main.nf
Gregor Sturm 906577873b
Bulk update modules to use versions.yml (#739)
* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-27 09:41:24 +01:00

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Text

// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process SNPSITES {
label 'process_medium'
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::snp-sites=2.5.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/snp-sites:2.5.1--hed695b0_0"
} else {
container "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
}
input:
path alignment
output:
path "*.fas" , emit: fasta
path "*.sites.txt" , emit: constant_sites
path "versions.yml" , emit: version
env CONSTANT_SITES, emit: constant_sites_string
script:
def software = getSoftwareName(task.process)
"""
snp-sites \\
$alignment \\
$options.args \\
> filtered_alignment.fas
echo \$(snp-sites -C $alignment) > constant.sites.txt
CONSTANT_SITES=\$(cat constant.sites.txt)
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(snp-sites -V 2>&1 | sed 's/snp-sites //')
END_VERSIONS
"""
}