nf-core_modules/modules/khmer/uniquekmers/main.nf
2022-06-30 16:23:30 +01:00

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process KHMER_UNIQUEKMERS {
tag "$fasta"
label 'process_low'
conda (params.enable_conda ? "bioconda::khmer=3.0.0a3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/khmer:3.0.0a3--py37haa7609a_2' :
'quay.io/biocontainers/khmer:3.0.0a3--py37haa7609a_2' }"
input:
path fasta
val kmer_size
output:
path "report.txt" , emit: report
path "kmers.txt" , emit: kmers
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
unique-kmers.py \\
-k $kmer_size \\
-R report.txt \\
$args \\
$fasta
grep ^number report.txt | sed 's/^.*:.[[:blank:]]//g' > kmers.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
khmer: \$( unique-kmers.py --version 2>&1 | grep ^khmer | sed 's/^khmer //;s/ .*\$//' )
END_VERSIONS
"""
}