Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/index_pdg_metadata/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 INDEX_PDG_METADATA { |
| kkonganti@11 | 2 tag "index_pdg_metadata.py" |
| kkonganti@11 | 3 label "process_pico" |
| 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 pdg_metadata |
| kkonganti@11 | 13 path pdg_ref_snp_metadata |
| kkonganti@11 | 14 path accs_all |
| kkonganti@11 | 15 path mlst_results |
| kkonganti@11 | 16 |
| kkonganti@11 | 17 output: |
| kkonganti@11 | 18 path "*.pickle" , emit: index |
| kkonganti@11 | 19 path 'versions.yml', emit: versions |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 when: |
| kkonganti@11 | 22 task.ext.when == null || task.ext.when |
| kkonganti@11 | 23 |
| kkonganti@11 | 24 script: |
| kkonganti@11 | 25 def args = task.ext.args ?: '' |
| kkonganti@11 | 26 def mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '') |
| kkonganti@11 | 27 """ |
| kkonganti@11 | 28 index_pdg_metadata.py \\ |
| kkonganti@11 | 29 $mlst_results \\ |
| kkonganti@11 | 30 -pdg_dir "." |
| kkonganti@11 | 31 |
| kkonganti@11 | 32 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 33 "${task.process}": |
| kkonganti@11 | 34 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 35 END_VERSIONS |
| kkonganti@11 | 36 """ |
| kkonganti@11 | 37 |
| kkonganti@11 | 38 } |