nf-core_modules/modules/vardictjava/main.nf
2022-06-27 10:35:41 +02:00

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process VARDICTJAVA {
tag "$meta.id"
label 'process_medium'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai), path(bed)
tuple path(fasta), path(fasta_fai)
output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '1.8.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
vardict-java \\
$args \\
-c 1 -S 2 -E 3 \\
-b $bam \\
-th $task.cpus \\
-N $prefix \\
-G $fasta \\
$bed \\
| teststrandbias.R \\
| var2vcf_valid.pl \\
$args2 \\
-N $prefix \\
| gzip -c > ${prefix}.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
vardict-java: $VERSION
var2vcf_valid.pl: \$(echo \$(var2vcf_valid.pl -h | sed -n 2p | awk '{ print \$2 }'))
END_VERSIONS
"""
}