mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 21:59:55 +00:00
feat: add process to standardize kraken report
This commit is contained in:
parent
4352d35937
commit
4f728648f5
1 changed files with 24 additions and 0 deletions
24
modules/local/kraken_standard_report.nf
Normal file
24
modules/local/kraken_standard_report.nf
Normal file
|
@ -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}"
|
||||||
|
"""
|
||||||
|
}
|
||||||
|
|
Loading…
Reference in a new issue