Mercurial > repos > kkonganti > cfsan_cronology
diff 0.2.0/modules/rmlst/main.nf @ 11:a5f31c44f8c9
planemo upload
author | kkonganti |
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date | Mon, 15 Jul 2024 16:11:44 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.2.0/modules/rmlst/main.nf Mon Jul 15 16:11:44 2024 -0400 @@ -0,0 +1,37 @@ +process RMLST_POST { + tag "${meta.id}" + label "process_pico" + maxForks 3 + + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/requests:2.26.0' : + 'quay.io/biocontainers/requests:2.26.0' }" + + input: + tuple val(meta), path(genome) + + output: + tuple val(meta), path('*.tsv') , emit: tsv, optional: true + tuple val(meta), path('*.log.json'), emit: log, optional: true + path 'versions.yml' , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = (task.ext.prefix ?: meta.id) + + """ + rmlst_post.py \\ + -fasta $genome \\ + -prefix $prefix \\ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$( python --version | sed 's/Python //g' ) + requests: \$( python -c "import requests; print (requests.__version__)" ) + END_VERSIONS + """ +} \ No newline at end of file