process VARDICTJAVA { tag "$meta.id" label 'process_medium' conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) container "${ 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) 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 ?: "${meta.id}" """ export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=$fasta"' 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: \$( realpath \$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//' ) var2vcf_valid.pl: \$( var2vcf_valid.pl -h | sed '2!d;s/.* //' ) END_VERSIONS """ }