mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
48 lines
1.6 KiB
Text
48 lines
1.6 KiB
Text
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
|
|
"""
|
|
}
|