diff --git a/modules/local/kraken_standard_report.nf b/modules/local/kraken_standard_report.nf new file mode 100644 index 0000000..93109aa --- /dev/null +++ b/modules/local/kraken_standard_report.nf @@ -0,0 +1,24 @@ +process KRAKEN_STANDARD_REPORT { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? 'conda-forge::sed=4.8' : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' + } else { + container 'biocontainers/biocontainers:v1.2.0_cv2' + } + + input: + tuple val(meta), path(report) + + output: + tuple val(meta), path(result), emit: report + + script: + result = "${report.baseName}_standardized.kraken2.report.txt" + """ + cut -f1-3,6-8 "${report}" > "${result}" + """ +} +