nf-core_modules/modules/bamtools/convert/main.nf

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process BAMTOOLS_CONVERT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::bamtools=2.5.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bamtools:2.5.1--h9a82719_9' :
'quay.io/biocontainers/bamtools:2.5.1--h9a82719_9' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.{bed,fasta,fastq,json,pileup,sam,yaml}"), emit: data
path "versions.yml" , emit: versions
2022-02-04 08:53:32 +00:00
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
m = args =~ /-format ([a-z]+)/
ext = m[0][1]
"""
bamtools \\
convert \\
$args \\
-in $bam \\
-out ${prefix}.${ext}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""
}