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eab173f2bb
* Added java options to vardict java * updated test.yml * correctly added java options * Added automatic version numbers for vardictjava * possible fix for version number in conda * removed the cram tests * linting * Update modules/vardictjava/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * Update modules/vardictjava/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * removed the version line Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
48 lines
1.5 KiB
Text
48 lines
1.5 KiB
Text
process VARDICTJAVA {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
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'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
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input:
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tuple val(meta), path(bam), path(bai), path(bed)
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path(fasta)
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path(fasta_fai)
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output:
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tuple val(meta), path("*.vcf.gz"), emit: vcf
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=$fasta"'
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vardict-java \\
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$args \\
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-c 1 -S 2 -E 3 \\
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-b $bam \\
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-th $task.cpus \\
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-N $prefix \\
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-G $fasta \\
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$bed \\
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| teststrandbias.R \\
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| var2vcf_valid.pl \\
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$args2 \\
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-N $prefix \\
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| gzip -c > ${prefix}.vcf.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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vardict-java: \$( realpath \$( command -v vardict-java ) | sed 's/.*java-//;s/-.*//' )
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var2vcf_valid.pl: \$( var2vcf_valid.pl -h | sed '2!d;s/.* //' )
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END_VERSIONS
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"""
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}
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