Merge pull request #300 from nf-core/fix_antismash_ampcombi

Fix pyrodigal channels, update ampcombi docs
nf-core · Aug 4, 2023 · 1e3649e · 1e3649e
2 parents fadc05c + 751fa03
commit 1e3649e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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`
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -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"
                 },

diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf
@@ -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, [], [] )