Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/custom/qual_passed_genomes/main.nf @ 14:9e80528263c4
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 17:32:05 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process QUAL_PASSED_GENOMES { |
| kkonganti@11 | 2 tag "Consolidate" |
| kkonganti@11 | 3 label "process_micro" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : |
| kkonganti@11 | 9 'quay.io/biocontainers/python:3.10.4' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 path acc_passed_tool1 |
| kkonganti@11 | 13 path acc_passed_tool2 |
| kkonganti@11 | 14 |
| kkonganti@11 | 15 output: |
| kkonganti@11 | 16 path 'accs_passed.txt', emit: accs |
| kkonganti@11 | 17 path 'versions.yml' , emit: versions |
| kkonganti@11 | 18 |
| kkonganti@11 | 19 when: |
| kkonganti@11 | 20 task.ext.when == null || task.ext.when |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 script: |
| kkonganti@11 | 23 def args = task.ext.args ?: '' |
| kkonganti@11 | 24 def prefix = task.index ?: '' |
| kkonganti@11 | 25 def output = 'accs_passed.txt' |
| kkonganti@11 | 26 |
| kkonganti@11 | 27 """ |
| kkonganti@11 | 28 qual_confirm.py \\ |
| kkonganti@11 | 29 -f1 $acc_passed_tool1 \\ |
| kkonganti@11 | 30 -f2 $acc_passed_tool2 |
| kkonganti@11 | 31 |
| kkonganti@11 | 32 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@11 | 33 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 34 END_VERSIONS |
| kkonganti@11 | 35 """ |
| kkonganti@11 | 36 } |