diff --git a/src/modules/kmc.nf b/src/modules/kmc.nf new file mode 100644 index 0000000000000000000000000000000000000000..a0f4997d819323c35ecda4264b0ed4bafc0aee91 --- /dev/null +++ b/src/modules/kmc.nf @@ -0,0 +1,30 @@ +/* + * normalize bam file + */ +process FASTKMERS { + tag "$meta.id" + label 'process_single' + publishDir "results/${meta.specie}/${meta.sex}/${meta.read}/", mode: 'copy' + + container "lbmc/kmc:3.2.2" + + input: + tuple val(meta), path(fastq) + + output: + tuple val(meta), path("*.csv"), emit: csv + path "versions.yml" , emit: versions + + script: + def args = task.ext.args ?: '' + """ + kmc -k31 ${fastq} 31mers . + kmc_tools transform 27mers dump ${fastq.simpleName}.txt + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + kmc: \$(echo \$(kmc --version 2>&1)) + END_VERSIONS + """ +}