nf-core_modules/modules/arriba/main.nf
2022-05-09 14:55:59 +02:00

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process ARRIBA {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::arriba=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/arriba:2.2.1--hecb563c_2' :
'quay.io/biocontainers/arriba:2.2.1--hecb563c_2' }"
input:
tuple val(meta), path(bam)
path fasta
path gtf
path blacklist
path known_fusions
path structural_variants
path tags
path protein_domains
output:
tuple val(meta), path("*.fusions.tsv") , emit: fusions
tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
def known_fusions = known_fusions ? "-k $known_fusions" : ""
def structural_variants = structural_variants ? "-d $structual_variants" : ""
def tags = tags ? "-t $tags" : ""
def protein_domains = protein_domains ? "-p $protein_domains" : ""
"""
arriba \\
-x $bam \\
-a $fasta \\
-g $gtf \\
-o ${prefix}.fusions.tsv \\
-O ${prefix}.fusions.discarded.tsv \\
$blacklist \\
$known_fusions \\
$structural_variants \\
$tags \\
$protein_domains \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
arriba: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo stub > ${prefix}.fusions.tsv
echo stub > ${prefix}.fusions.discarded.tsv
echo "${task.process}:" > versions.yml
echo ' arriba: 2.2.1' >> versions.yml
"""
}