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Co-authored-by: Matthias Hörtenhuber <[email protected]>

Author: jasmezz

CHANGELOG.md

@@ -24,6 +24,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
+- FastQC
+
 ## v1.1.3 - [2023-08-11]
 
 ### `Added`

docs/usage.md

@@ -230,7 +230,9 @@ Note that the names of the supplied folders must differ from each other (e.g. `a
 
 ### DeepBGC
 
-> ⚠️ The dependencies for the deepBGC database download are currently broken. Until deepBGC gets fixed, users need to provide the database files themselves or just skip the tool (`--bgc_skip_deepbgc`). To provide the files yourself: The links for the database files can be found in [this script](https://github.com/Merck/deepbgc/blob/476934b61521d23c1122a1cfada176ee5e402741/deepbgc/data.py) from the deepBGC GitHub repository. The command `deepbgc download` as described below will not work at the moment.
+:::danger
+The dependencies for the deepBGC database download are currently broken. Until deepBGC gets fixed, users need to provide the database files themselves or just skip the tool (`--bgc_skip_deepbgc`). To provide the files yourself: The links for the database files can be found in [this script](https://github.com/Merck/deepbgc/blob/476934b61521d23c1122a1cfada176ee5e402741/deepbgc/data.py) from the deepBGC GitHub repository. The command `deepbgc download` as described below will not work at the moment.
+:::
 
 DeepBGC relies on trained models and Pfams to run its analysis. nf-core/funcscan will download these databases for you. If the flag `--save_databases` is set, the downloaded files will be stored in the output directory under `databases/deepbgc/`.
 

nextflow_schema.json

@@ -311,6 +311,7 @@
                 },
                 "annotation_prokka_retaincontigheaders": {
                     "type": "boolean",
+                    "fa_icon":"fas fa-remove-format",          
                     "help_text": "This parameter allows prokka to retain the original contig names by activating `PROKKA`'s  `--force` flag. If this parameter is set to `false` it activates `PROKKA`'s flags `--locus-tag PROKKA --centre CENTER` so the locus tags (contig names) will be PROKKA_# and the center tag will be CENTER. By default `PROKKA` changes contig headers to avoid errors that might rise due to long contig headers, so this must be turned on if the user has short contig names that should be retained by `PROKKA`. \n\n> Modifies tool parameter(s):\n> - Prokka: `--locus-tag PROKKA --centre CENTER`\n> - Prokka: `--force`",
                     "description": "Retains contig names."
                 }