--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/prodigal/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,56 @@
+process PRODIGAL {
+    tag "$meta.id"
+    label 'process_nano'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}prodigal${params.fs}2.6.3" : null)
+    conda (params.enable_conda ? "bioconda::prodigal=2.6.3 conda-forge::pigz=2.6" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' :
+        'quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0' }"
+
+    input:
+        tuple val(meta), path(genome)
+        val(output_format)
+
+    output:
+        tuple val(meta), path("*.${output_format}"), emit: gene_annotations
+        tuple val(meta), path("*.fna")             , emit: cds
+        tuple val(meta), path("*.faa")             , emit: proteins
+        tuple val(meta), path("*_all.txt")         , emit: all_gene_annotations
+        tuple val(meta), path("*trn")              , emit: trained, 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}"
+        def training      = args.toString().matches(/.*-t/) ? "-t ${prefix}.trn" : ''
+        args              = args.toString().replace(/-t/, '')
+        """
+        if [ "$training" = "-t ${prefix}.trn" ]; then
+            touch "${prefix}.fna"
+            touch "${prefix}.faa"
+            touch "${prefix}_all.txt"
+            touch "${prefix}.${output_format}"
+
+            prodigal \\
+                $training \\
+                -i $genome
+        fi
+
+        prodigal \\
+            $args \\
+            -d "${prefix}.fna" \\
+            -o "${prefix}.${output_format}" \\
+            -a "${prefix}.faa" \\
+            -s "${prefix}_all.txt" \\
+            -i $genome
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            prodigal: \$(prodigal -v 2>&1 | sed -n 's/Prodigal V\\(.*\\):.*/\\1/p')
+        END_VERSIONS
+        """
+}
\ No newline at end of file