Stop prokka from renaming contigs by default

CHANGELOG.md

@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.1.4dev - [unreleased]
+
+### `Added`
+
+### `Fixed`
+
+- [###]() Added new parameter `annotation_prokka_retaincontigheaders` to allow prokka to retain the original contig headers/locus tag. (by @darcy220606)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## v1.1.3 - [2023-08-11]
 
 ### `Added`

conf/modules.config

@@ -65,8 +65,7 @@ process {
             "--mincontiglen ${params.annotation_prokka_mincontiglen}",
             "--evalue ${params.annotation_prokka_evalue}",
             "--coverage ${params.annotation_prokka_coverage}",
-            "--centre ${params.annotation_prokka_centre}",
-            "--locustag ${params.annotation_prokka_locustag}",
+            params.annotation_prokka_retaincontigheaders ? "--force" : "--locustag PROKKA --centre CENTER" ,
             params.annotation_prokka_singlemode ? '' : '--metagenome' ,
             params.annotation_prokka_cdsrnaolap ? '--cdsrnaolap' : '',
             params.annotation_prokka_rawproduct ? '--rawproduct' : '',

nextflow.config

@@ -62,10 +62,9 @@ params {
     annotation_prokka_mincontiglen          = 1
     annotation_prokka_evalue                = 1E-06
     annotation_prokka_coverage              = 80
-    annotation_prokka_centre                = null
-    annotation_prokka_compliant             = false
-    annotation_prokka_locustag              = 'PROKKA'
+    annotation_prokka_compliant             = true
     annotation_prokka_addgenes              = false
+    annotation_prokka_retaincontigheaders   = false
 
     // Database downloading options
     save_databases                          = false

nextflow_schema.json

@@ -297,30 +297,22 @@
                     "help_text": "Activates [RNAmmer](https://services.healthtech.dtu.dk/service.php?RNAmmer-1.2) instead of the Prokka default [Barrnap](https://github.com/tseemann/barrnap) for rRNA prediction during the annotation process. RNAmmer classifies ribosomal RNA genes in genome sequences by using two levels of Hidden Markov Models. Barrnap uses the nhmmer tool that includes HMMER 3.1 for HMM searching in RNA:DNA style.\n\nFor more information please check Prokka [documentation](https://github.com/tseemann/prokka).\n\n> Modifies tool parameter(s):\n> - Prokka: `--rnammer`",
                     "fa_icon": "fas fa-adjust"
                 },
-                "annotation_prokka_centre": {
-                    "type": "string",
-                    "description": "Sequencing centre ID.",
-                    "fa_icon": "fas fa-map-marker-alt",
-                    "help_text": "Add the sequencing center ID used in generating the raw sequences. This flag is typically requested in combination with the `--compliant` flag when contigs need to be renamed due to non-conforming contig headers. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--centre`"
-                },
                 "annotation_prokka_compliant": {
                     "type": "boolean",
                     "fa_icon": "far fa-check-circle",
                     "description": "Force contig name to Genbank/ENA/DDJB naming rules.",
                     "help_text": "Force the contig headers to conform to the Genbank/ENA/DDJB contig header standards. This is activated in combination with `--centre [X]` when contig headers supplied by the user are non-conforming and therefore need to be renamed before Prokka can start annotation. This flag activates  `--genes --mincontiglen 200`. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--compliant`"
                 },
-                "annotation_prokka_locustag": {
-                    "type": "string",
-                    "default": "Prokka",
-                    "fa_icon": "fas fa-tags",
-                    "description": "Assign the locus tag for the contig header.",
-                    "help_text": "Assign a special name to the contig. This is used when a specific group of samples are run in a batch. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--locustag`"
-                },
                 "annotation_prokka_addgenes": {
                     "type": "boolean",
                     "fa_icon": "fas fa-dna",
                     "description": "Add the gene features for each CDS hit.",
                     "help_text": "For every CDS annotated, this flag adds the gene that encodes for that CDS region. For more information please check Prokka [documentation](https://github.com/tseemann/prokka). \n\n> Modifies tool parameter(s):\n> - Prokka: `--addgenes`"
+                },
+                "annotation_prokka_retaincontigheaders": {
+                    "type": "boolean",
+                    "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s  `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
+                    "description": "Retains contig names."
                 }
             },
             "fa_icon": "fas fa-tools",