Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/modules/download_pdg_metadata/main.nf @ 7:f02f143c02fb
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 20:24:38 -0500 |
| parents | c8597e9e1a97 |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process DOWNLOAD_PDG_METADATA { |
| kkonganti@0 | 2 tag "dl_pdg_metadata.py" |
| kkonganti@0 | 3 label "process_pico" |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) |
| kkonganti@0 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@0 | 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : |
| kkonganti@0 | 9 'quay.io/biocontainers/python:3.10.4' }" |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 input: |
| kkonganti@0 | 12 val pdg_release |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 output: |
| kkonganti@0 | 15 path "**${params.fs}*.metadata.tsv" , emit: pdg_metadata |
| kkonganti@0 | 16 path "**${params.fs}*.reference_target.cluster_list.tsv", emit: snp_cluster_metadata |
| kkonganti@0 | 17 path "**${params.fs}*accs_all.txt" , emit: accs |
| kkonganti@0 | 18 path 'versions.yml' , emit: versions |
| kkonganti@0 | 19 |
| kkonganti@0 | 20 when: |
| kkonganti@0 | 21 task.ext.when == null || task.ext.when |
| kkonganti@0 | 22 |
| kkonganti@0 | 23 script: |
| kkonganti@0 | 24 def args = task.ext.args ?: '' |
| kkonganti@0 | 25 args += (pdg_release ? " -rel ${pdg_release}" : '') |
| kkonganti@0 | 26 args += (params.pdg_org ? " -org ${params.pdg_org}" : '') |
| kkonganti@0 | 27 """ |
| kkonganti@0 | 28 dl_pdg_metadata.py \\ |
| kkonganti@0 | 29 $args |
| kkonganti@0 | 30 |
| kkonganti@0 | 31 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 32 "${task.process}": |
| kkonganti@0 | 33 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@0 | 34 END_VERSIONS |
| kkonganti@0 | 35 """ |
| kkonganti@0 | 36 |
| kkonganti@0 | 37 } |