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CHANGELOG.md

@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#381](https://github.com/nf-core/funcscan/pull/381) Added support for supplying pre-annotated sequences to the pipeline. (by @jfy133, @jasmezz)
 - [#382](https://github.com/nf-core/funcscan/pull/382) Optimised BGC screening run time and prevent crashes due to too-short contigs by adding contig length filtering for BGC workflow only. (by @jfy133, @darcy220606)
 - [#366](https://github.com/nf-core/funcscan/pull/366) Added nf-test on pipeline level. (by @jfy133, @Darcy220606, @jasmezz)
+- [#403](https://github.com/nf-core/funcscan/pull/403) Added antiSMASH parameters `--pfam2go`, `--rre`, and `--tfbs`. (reported by @Darcy220606, added by @jasmezz)
 
 ### `Fixed`
 

conf/modules.config

@@ -412,6 +412,9 @@ process {
             params.bgc_antismash_smcogtrees ? '--smcog-trees' : '',
             params.bgc_antismash_ccmibig ? '--cc-mibig' : '',
             params.bgc_antismash_cbsubclusters ? '--cb-subclusters' : '',
+            params.bgc_antismash_pfam2go ? '--pfam2go' : '',
+            params.bgc_antismash_rre ? '--rre' : '',
+            params.bgc_antismash_tfbs ? '--tfbs' : '',
             "--allow-long-headers",
             "--minlength ${params.bgc_antismash_contigminlength}",
             "--hmmdetection-strictness ${params.bgc_antismash_hmmdetectionstrictness}",

nextflow_schema.json

@@ -1180,14 +1180,14 @@
                     "type": "boolean",
                     "default": "false",
                     "description": "Run Pfam to Gene Ontology mapping module.",
-                    "help_text": "For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--pfam2go`",
+                    "help_text": "This maps the proteins to Pfam database to annotate BGC modules with functional information based on the protein families they contain. For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--pfam2go`",
                     "fa_icon": "fas fa-search"
                 },
                 "bgc_antismash_rre": {
                     "type": "boolean",
                     "default": "false",
                     "description": "Run RREFinder precision mode on all RiPP gene clusters.",
-                    "help_text": "For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--rre`",
+                    "help_text": "This enables the prediction of regulatory elements on the BGC that help in the control of protein expression. For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--rre`",
                     "fa_icon": "fas fa-search"
                 },
                 "bgc_antismash_taxon": {
@@ -1202,7 +1202,7 @@
                     "type": "boolean",
                     "default": "false",
                     "description": "Run TFBS finder on all gene clusters.",
-                    "help_text": "For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--tfbs`",
+                    "help_text": "This enables the prediction of transcription factor binding sites which control the gene expression. For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--tfbs`",
                     "fa_icon": "fas fa-search"
                 }
             },