Gecco convert

conf/modules.config

@@ -529,6 +529,14 @@ process {
         ].join(' ').trim()
     }
 
+     withName: GECCO_CONVERT {
+        publishDir = [
+            path: { "${params.outdir}/bgc/gecco/${meta.id}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
     withName: HAMRONIZATION_ABRICATE {
         publishDir = [
             path: { "${params.outdir}/arg/hamronization/abricate" },

nextflow.config

@@ -250,6 +250,9 @@ params {
     bgc_gecco_pfilter                               = 1E-9
     bgc_gecco_edgedistance                          = 0
     bgc_gecco_mask                                  = false
+    run_gecco_convert                               = false
+    gecco_convert_mode                              = 'clusters'
+    gecco_convert_format                            = 'gff'
 
     bgc_run_hmmsearch                               = false
     bgc_hmmsearch_models                            = null
@@ -258,7 +261,7 @@ params {
     bgc_hmmsearch_savedomains                       = false
 
     // Schema validation default options
-    validate_params                                 = true
+    validate_params                                 = true   
 }
 
 // Load base.config by default for all pipelines

nextflow_schema.json

@@ -1418,6 +1418,34 @@
             },
             "fa_icon": "fas fa-angle-double-right"
         },
+
+        "gecco_options": {
+            "title": "GECCO biosynthetic gene cluster prediction options",
+            "type": "object",
+            "description": "Parameters for running GECCO BGC prediction",
+            "default": "",
+            "properties": {
+                "run_gecco_convert": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Enable conversion of contig FASTA files to GECCO-compatible format.",
+                    "help_text": "GECCO requires contig FASTA files to be in a specific format. Enabling this option will convert the input FASTA files to the required format before running GECCO.\n\n> Modifies tool parameter(s):\n> - gecco convert: `--enable`"
+                },
+                "gecco_convert_mode": {
+                    "type": "string",
+                    "default": "clusters",
+                    "description": "Mode for converting contig FASTA files for GECCO.",
+                    "help_text": "Select the mode for converting contig FASTA files. 'default' uses standard conversion settings, while 'custom' allows for user-defined parameters.\n\n> Modifies tool parameter(s):\n> - gecco convert: `--mode`"
+                },
+                "gecco_convert_format": {
+                    "type": "string",
+                    "default": "gff",
+                    "description": "Output format for converted contig files.",
+                    "help_text": "Specify the output format for the converted contig files. Options include 'fasta' and 'genbank'.\n\n> Modifies tool parameter(s):\n> - gecco convert: `--format`"
+                }
+            },
+            "fa_icon": "fas fa-angle-double-right"
+        },
         "bgc_hmmsearch": {
             "title": "BGC: hmmsearch",
             "type": "object",
@@ -1703,6 +1731,9 @@
         {
             "$ref": "#/$defs/bgc_gecco"
         },
+        {
+            "$ref": "#/$defs/gecco_options"
+        },
         {
             "$ref": "#/$defs/bgc_hmmsearch"
         },

subworkflows/local/bgc.nf

@@ -12,6 +12,7 @@ include { DEEPBGC_PIPELINE                       } from '../../modules/nf-core/d
 include { COMBGC                                 } from '../../modules/local/combgc'
 include { TABIX_BGZIP as BGC_TABIX_BGZIP         } from '../../modules/nf-core/tabix/bgzip/main'
 include { MERGE_TAXONOMY_COMBGC                  } from '../../modules/local/merge_taxonomy_combgc'
+include { GECCO_CONVERT                          } from '../../modules/nf-core/gecco/convert/main'
 
 workflow BGC {
     take:
@@ -104,6 +105,18 @@ workflow BGC {
         ch_bgcresults_for_combgc = ch_bgcresults_for_combgc.mix(ch_geccoresults_for_combgc)
     }
 
+    // GECCO CONVERT
+    if (params.run_gecco_convert) {
+        ch_gecco_clusters_and_gbk = GECCO_RUN.out.clusters
+            .join(GECCO_RUN.out.gbk)
+            .map { meta, clusters_file, gbk_file ->
+                [ meta, clusters_file, gbk_file ]
+            }
+        ch_gecco_mode = Channel.value( params.gecco_convert_mode)
+        ch_gecco_format = Channel.value( params.gecco_convert_format)
+
+        GECCO_CONVERT(ch_gecco_clusters_and_gbk, ch_gecco_mode, ch_gecco_format)
+    }
     // HMMSEARCH
     if (params.bgc_run_hmmsearch) {
         if (params.bgc_hmmsearch_models) {