Mercurial > repos > kkonganti > cfsan_bettercallsal
diff 0.5.0/modules/download_pdg_metadata/main.nf @ 1:365849f031fd
"planemo upload"
author | kkonganti |
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date | Mon, 05 Jun 2023 18:48:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/0.5.0/modules/download_pdg_metadata/main.nf Mon Jun 05 18:48:51 2023 -0400 @@ -0,0 +1,36 @@ +process DOWNLOAD_PDG_METADATA { + tag "dl_pdg_metadata.py" + label "process_pico" + + module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) + conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/python:3.10.4' : + 'quay.io/biocontainers/python:3.10.4' }" + + input: + val pdg_release + + output: + path "**${params.fs}*.metadata.tsv" , emit: pdg_metadata + path "**${params.fs}*.reference_target.cluster_list.tsv", emit: snp_cluster_metadata + path "**${params.fs}*accs_all.txt" , emit: accs + path 'versions.yml' , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + args += (pdg_release ? " -rel ${pdg_release}" : '') + """ + dl_pdg_metadata.py \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + python: \$( python --version | sed 's/Python //g' ) + END_VERSIONS + """ + +} \ No newline at end of file