nf-core_modules/modules/samtools/flagstat/main.nf
Harshil Patel e751e5040a
Bump software versions for viralrecon modules (#1198)
* Bump software versions for viralrecon modules

* Remove custom params.save_unaligned from bowtie2_align

* Unify samtools modules and error if input and output names are the same

* Fix ALL the tests
2022-01-07 17:52:39 +00:00

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process SAMTOOLS_FLAGSTAT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0' :
'quay.io/biocontainers/samtools:1.14--hb421002_0' }"
input:
tuple val(meta), path(bam), path(bai)
output:
tuple val(meta), path("*.flagstat"), emit: flagstat
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
"""
samtools \\
flagstat \\
--threads ${task.cpus-1} \\
$bam \\
> ${bam}.flagstat
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}