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Added antismash params: pfam2go, rre, tfbs #403

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Jul 19, 2024
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3 changes: 3 additions & 0 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -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
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21 changes: 21 additions & 0 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
Expand Up @@ -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": "For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--pfam2go`",
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"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`",
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"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": "For more information see the antiSMASH [documentation](https://docs.antismash.secondarymetabolites.org/).\n\n> Modifies tool parameter(s):\n> - antiSMASH: `--tfbs`",
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"fa_icon": "fas fa-search"
}
},
"fa_icon": "fa fa-sliders"
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