Merge pull request #403 from nf-core/add-antismash-parameters

Added antismash params: pfam2go, rre, tfbs

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.config

@@ -204,7 +204,10 @@ params {
     bgc_antismash_ccmibig                            = false
     bgc_antismash_contigminlength                    = 3000
     bgc_antismash_hmmdetectionstrictness             = 'relaxed'
+    bgc_antismash_pfam2go                            = false
+    bgc_antismash_rre                                = false
     bgc_antismash_taxon                              = 'bacteria'
+    bgc_antismash_tfbs                               = false
 
     bgc_skip_deepbgc                                 = false
     bgc_deepbgc_db                                   = null

nextflow_schema.json

@@ -1176,13 +1176,34 @@
                     "fa_icon": "fas fa-search",
                     "enum": ["relaxed", "strict", "loose"]
                 },
+                "bgc_antismash_pfam2go": {
+                    "type": "boolean",
+                    "default": "false",
+                    "description": "Run Pfam to Gene Ontology mapping module.",
+                    "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": "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": {
                     "type": "string",
                     "default": "bacteria",
                     "description": "Specify which taxonomic classification of input sequence to use.",
                     "help_text": "This specifies which set of secondary metabolites to screen for, based on the taxon type the secondary metabolites are from.\n\nThis will run different pipelines depending on whether the input sequences are from bacteria or fungi.\n\nFor more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--taxon`",
                     "fa_icon": "fas fa-bacteria",
                     "enum": ["bacteria", "fungi"]
+                },
+                "bgc_antismash_tfbs": {
+                    "type": "boolean",
+                    "default": "false",
+                    "description": "Run TFBS finder on all gene clusters.",
+                    "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"
                 }
             },
             "fa_icon": "fa fa-sliders"