Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/rmlst/main.nf @ 11:a5f31c44f8c9
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:11:44 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process RMLST_POST { |
| kkonganti@11 | 2 tag "${meta.id}" |
| kkonganti@11 | 3 label "process_pico" |
| kkonganti@11 | 4 maxForks 3 |
| kkonganti@11 | 5 |
| kkonganti@11 | 6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@11 | 7 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null) |
| kkonganti@11 | 8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 9 'https://depot.galaxyproject.org/singularity/requests:2.26.0' : |
| kkonganti@11 | 10 'quay.io/biocontainers/requests:2.26.0' }" |
| kkonganti@11 | 11 |
| kkonganti@11 | 12 input: |
| kkonganti@11 | 13 tuple val(meta), path(genome) |
| kkonganti@11 | 14 |
| kkonganti@11 | 15 output: |
| kkonganti@11 | 16 tuple val(meta), path('*.tsv') , emit: tsv, optional: true |
| kkonganti@11 | 17 tuple val(meta), path('*.log.json'), emit: log, optional: true |
| kkonganti@11 | 18 path 'versions.yml' , emit: versions |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 when: |
| kkonganti@11 | 21 task.ext.when == null || task.ext.when |
| kkonganti@11 | 22 |
| kkonganti@11 | 23 script: |
| kkonganti@11 | 24 def prefix = (task.ext.prefix ?: meta.id) |
| kkonganti@11 | 25 |
| kkonganti@11 | 26 """ |
| kkonganti@11 | 27 rmlst_post.py \\ |
| kkonganti@11 | 28 -fasta $genome \\ |
| kkonganti@11 | 29 -prefix $prefix \\ |
| kkonganti@11 | 30 |
| kkonganti@11 | 31 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 32 "${task.process}": |
| kkonganti@11 | 33 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 34 requests: \$( python -c "import requests; print (requests.__version__)" ) |
| kkonganti@11 | 35 END_VERSIONS |
| kkonganti@11 | 36 """ |
| kkonganti@11 | 37 } |