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

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process NUCMER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' :
'quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12' }"
input:
tuple val(meta), path(ref), path(query)
output:
tuple val(meta), path("*.delta") , emit: delta
tuple val(meta), path("*.coords"), emit: coords
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false
def is_compressed_query = query.getName().endsWith(".gz") ? true : false
def fasta_name_ref = ref.getName().replace(".gz", "")
def fasta_name_query = query.getName().replace(".gz", "")
"""
if [ "$is_compressed_ref" == "true" ]; then
gzip -c -d $ref > $fasta_name_ref
fi
if [ "$is_compressed_query" == "true" ]; then
gzip -c -d $query > $fasta_name_query
fi
nucmer \\
-p $prefix \\
--coords \\
$args \\
$fasta_name_ref \\
$fasta_name_query
cat <<-END_VERSIONS > versions.yml
"${task.process}":
nucmer: \$( nucmer --version 2>&1 | grep "version" | sed -e "s/NUCmer (NUCleotide MUMmer) version //g; s/nucmer//g;" )
END_VERSIONS
"""
}