--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/modules/otf_genome/main.nf	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,38 @@
+process OTF_GENOME {
+    tag "$meta.id"
+    label "process_pico"
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
+    conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/python:3.10.4' :
+        'quay.io/biocontainers/python:3.10.4' }"
+
+    input:
+        tuple val(meta), path(kma_hits)
+
+    output:
+        tuple val(meta), path('*_scaffolded_genomic.fna.gz'), emit: genomes_fasta, optional: true
+        path '*FAILED.txt'                                  , emit: failed, optional: true
+        path 'versions.yml'                                 , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}"
+        args += (kma_hits ? " -txt ${kma_hits}" : '')
+        args += (params.tuspy_gd ? " -gd ${params.tuspy_gd}" : '')
+        args += (prefix ? " -op ${prefix}" : '')
+
+        """
+        gen_otf_genome.py \\
+            $args
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            python: \$( python --version | sed 's/Python //g' )
+        END_VERSIONS
+        """
+}
\ No newline at end of file