nf-core_modules/modules/ismapper/main.nf
2022-02-04 09:53:32 +01:00

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process ISMAPPER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::ismapper=2.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ismapper:2.0.2--pyhdfd78af_1' :
'quay.io/biocontainers/ismapper:2.0.2--pyhdfd78af_1' }"
input:
tuple val(meta), path(reads), path(reference), path(query)
output:
tuple val(meta), path("results/*"), emit: results
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}"
"""
ismap \\
$args \\
--t $task.cpus \\
--output_dir results \\
--queries $query \\
--reference $reference \\
--reads $reads
cat <<-END_VERSIONS > versions.yml
"${task.process}":
ismapper: \$( echo \$( ismap --version 2>&1 ) | sed 's/^.*ismap //' )
END_VERSIONS
"""
}