--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.1.0/modules/prokka/main.nf	Mon Nov 27 12:37:44 2023 -0500
@@ -0,0 +1,55 @@
+process PROKKA {
+    tag "$meta.id"
+    label 'process_low'
+
+    module (params.enable_module ? "${params.swmodulepath}${params.fs}prokka${params.fs}1.14.6" : null)
+    conda (params.enable_conda ? "bioconda::prokka=1.14.6 conda-forge::perl" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' :
+        'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
+
+    input:
+        tuple val(meta), path(fasta), path(proteins), path(prodigal_tf)
+
+    output:
+        tuple val(meta), path("${prefix}/*.gff"), emit: gff
+        tuple val(meta), path("${prefix}/*.gbk"), emit: gbk
+        tuple val(meta), path("${prefix}/*.fna"), emit: fna
+        tuple val(meta), path("${prefix}/*.faa"), emit: faa
+        tuple val(meta), path("${prefix}/*.ffn"), emit: ffn
+        tuple val(meta), path("${prefix}/*.sqn"), emit: sqn
+        tuple val(meta), path("${prefix}/*.fsa"), emit: fsa
+        tuple val(meta), path("${prefix}/*.tbl"), emit: tbl
+        tuple val(meta), path("${prefix}/*.err"), emit: err
+        tuple val(meta), path("${prefix}/*.log"), emit: log
+        tuple val(meta), path("${prefix}/*.txt"), emit: txt
+        tuple val(meta), path("${prefix}/*.tsv"), emit: tsv
+        path "versions.yml" , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+        def args         = task.ext.args   ?: ''
+        def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
+        def prodigal_tf  = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
+        def prefix_l     = "${meta.id}" ?: ''
+        prefix           = task.ext.prefix ?: "${meta.id}"
+        def strain       = !params.prokka_strain && prefix_l ? "--strain '${prefix_l}'" : ''
+
+        """
+        prokka \\
+            $strain \\
+            $args \\
+            --cpus $task.cpus \\
+            --prefix $prefix \\
+            $proteins_opt \\
+            $prodigal_tf \\
+            $fasta
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
+        END_VERSIONS
+        """
+}
\ No newline at end of file