nf-core_modules/modules/samtools/faidx/main.nf
Ramprasad Neethiraj 49b18b1639
add stub to modules used in raredisease pipeline (#1206)
* add stub section

* add stub for bcftools norm

* add stub to more modules

* fix expansionhunter tests

* revert changes -picard

* Update stub to write version no.s to a file

* add picard

* revert picard again

* add stubs to more modules

* fix bwamem2

* add bcftools view

* add stubs

* fix svdb query

* review suggestions
2022-03-28 17:48:39 +02:00

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Text

process SAMTOOLS_FAIDX {
tag "$fasta"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path ("*.fai"), emit: fai
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
samtools \\
faidx \\
$fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
stub:
"""
touch ${fasta}.fai
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}