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feat: add process to standardize kraken report

This commit is contained in:
Moritz E. Beber 2022-10-14 10:56:14 +02:00
parent 4352d35937
commit 4f728648f5

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@ -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}"
"""
}