You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
49 lines
1.6 KiB
Plaintext
49 lines
1.6 KiB
Plaintext
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
|
|
"""
|
|
}
|