mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-15 06:23:09 +00:00
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process KRONA_CLEANUP {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
|
|
'biocontainers/biocontainers:v1.2.0_cv1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
|
|
|
|
output:
|
|
tuple val(meta), path("*.txt"), emit: txt
|
|
path "versions.yml", emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
"""
|
|
# Copy the file to a new name
|
|
cp ${krona} ${prefix}.txt
|
|
|
|
# Remove ugly 'x__' prefixes for each of the taxonomic levels
|
|
LEVELS=(d k p c o f g s)
|
|
for L in "\${LEVELS[@]}"; do
|
|
sed -i "s/\${L}__//g" ${prefix}.txt
|
|
done
|
|
|
|
# Remove underscores that are standing in place of spaces
|
|
sed -i "s/_/ /g" ${prefix}.txt
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
|
|
END_VERSIONS
|
|
"""
|
|
}
|