diff 0.5.0/modules/download_pdg_metadata/main.nf @ 1:365849f031fd

"planemo upload"
author kkonganti
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
+        """
+
+}
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