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Fix pyrodigal channels, update ampcombi docs #300

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Aug 4, 2023
Merged

Fix pyrodigal channels, update ampcombi docs #300

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31269c4
Fix pyrodigal channels, update ampcombi docs
jasmezz Aug 4, 2023
288935d
Update changelog
jasmezz Aug 4, 2023
751fa03
Update changelog
jasmezz Aug 4, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
- [#297](https://github.com/nf-core/funcscan/pull/297) Added check for empty annotation files prior going into screening. (❤️ to @alexhbnr for requesting, added by @jfy133)
- [#299](https://github.com/nf-core/funcscan/pull/299) Fixed pigz error with symlinks in Pyrodigal. (by @jasmezz)
- [#300](https://github.com/nf-core/funcscan/pull/300) Fixed wrong Pyrodigal channels being submitted to antiSMASH. (reported by Till Bayer, fix by @jasmezz)

### `Dependencies`

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4 changes: 2 additions & 2 deletions nextflow_schema.json
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Expand Up @@ -522,8 +522,8 @@
"properties": {
"amp_ampcombi_db": {
"type": "string",
"description": "Path to AMPcombi reference database directory.",
"help_text": "Path to the folder containing the reference database files:\n1. a fasta file with a `.fasta` file extension\n2. the corresponding table with with functional and taxonomic classifications in `.tsv` file extension.\n\nFor more information check AMPcombi [documentation](https://github.com/Darcy220606/AMPcombi).",
"description": "Path to AMPcombi reference database directory (DRAMP).",
"help_text": "AMPcombi uses the 'general AMPs' dataset of the (DRAMP database)[http://dramp.cpu-bioinfor.org/downloads/] for taxonomic classification. If you have a local version of it, you can provide the path to the folder containing the reference database files:\n1. a fasta file with a `.fasta` file extension\n2. the corresponding table with with functional and taxonomic classifications in `.tsv` file extension.\n\nFor more information check AMPcombi [documentation](https://github.com/Darcy220606/AMPcombi).",
"default": "None",
"fa_icon": "fas fa-address-book"
},
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4 changes: 2 additions & 2 deletions workflows/funcscan.nf
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Expand Up @@ -195,8 +195,8 @@ workflow FUNCSCAN {
GUNZIP_PYRODIGAL_GFF ( PYRODIGAL.out.gff )
ch_versions = ch_versions.mix(PYRODIGAL.out.versions)
ch_annotation_faa = GUNZIP_PYRODIGAL_FAA.out.gunzip
ch_annotation_fna = GUNZIP_PYRODIGAL_FAA.out.gunzip
ch_annotation_gff = GUNZIP_PYRODIGAL_FAA.out.gunzip
ch_annotation_fna = GUNZIP_PYRODIGAL_FNA.out.gunzip
ch_annotation_gff = GUNZIP_PYRODIGAL_GFF.out.gunzip
ch_annotation_gbk = Channel.empty() // Pyrodigal doesn't produce GBK
} else if ( params.annotation_tool == "prokka" ) {
PROKKA ( ch_prepped_input, [], [] )
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