nf-core_modules/modules/isoseq3/refine/main.nf
2022-07-07 11:10:18 +01:00

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process ISOSEQ3_REFINE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::isoseq3=3.4.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/isoseq3:3.4.0--0' :
'quay.io/biocontainers/isoseq3:3.4.0--0' }"
input:
tuple val(meta), path(bam)
path primers
output:
tuple val(meta), path("*.bam") , emit: bam
tuple val(meta), path("*.bam.pbi") , emit: pbi
tuple val(meta), path("*.consensusreadset.xml"), emit: consensusreadset
tuple val(meta), path("*.filter_summary.json") , emit: summary
tuple val(meta), path("*.report.csv") , emit: report
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}"
"""
isoseq3 \\
refine \\
-j $task.cpus \\
$args \\
$bam \\
$primers \\
${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
isoseq3: \$( isoseq3 refine --version|sed 's/isoseq refine //'|sed 's/ (commit.\\+//' )
END_VERSIONS
"""
}