--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/modules/index_pdg_metadata/main.nf	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,38 @@
+process INDEX_PDG_METADATA {
+    tag "index_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:
+        path pdg_metadata
+        path pdg_ref_snp_metadata
+        path accs_all
+        path mlst_results
+
+    output:
+        path "*.pickle"    , emit: index
+        path 'versions.yml', emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '')
+        """
+        index_pdg_metadata.py \\
+            $mlst_results \\
+            -pdg_dir "."
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            python: \$( python --version | sed 's/Python //g' )
+        END_VERSIONS
+        """
+
+}
\ No newline at end of file