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Co-authored-by: Kevin L. Keys <[email protected]>
Co-authored-by: Daniel Lundin <[email protected]>

bin/ampcombi_download.py

@@ -68,7 +68,7 @@ def download_DRAMP(db):
                 "T",
                 "V",
                 "W",
-                ",Y",
+                "Y"
             ]
             new = "".join(i for i in sequence if i in letters)
             f.write(">" + id + "\n" + new + "\n")

docs/output.md

@@ -130,7 +130,7 @@ Output Summaries:
 
 </details>
 
-[Pyrodigal](https://github.com/althonos/pyrodigal) annotates whole (meta-)genomes by identifying ORFs in a set of genomic DNA sequences. It produces the same results as [Prodigal](#prodigal) while being more resource-optimized, thus faster. Other than Prodigal, Pyrodigal cannot produce output in GenBank format. The output is used by some of the functional screening tools.
+[Pyrodigal](https://github.com/althonos/pyrodigal) annotates whole (meta-)genomes by identifying ORFs in a set of genomic DNA sequences. It produces the same results as [Prodigal](#prodigal) while being more resource-optimized, thus faster. Unlike Prodigal, Pyrodigal cannot produce output in GenBank format. The output is used by some of the functional screening tools.
 
 #### Prokka
 

docs/usage.md

@@ -82,7 +82,7 @@ To prevent entire pipeline failures due to a single 'bad sample', nf-core/funcsc
 
 When the annotation is run with Prokka, the resulting `.gbk` file passed to antiSMASH may produce the error `translation longer than location allows` and end the pipeline run. This Prokka bug has been reported before (see [discussion on GitHub](https://github.com/antismash/antismash/discussions/450)) and is not likely to be fixed soon.
 
-> ⚠️ If antiSMASH is run for BGC detection, we recommend to **not** run Prokka for annotation but instead use the default annotation tool (Pyrodigal) or switch to Prodigal, or Bakta (the latter to bacteria only!).
+> ⚠️ If antiSMASH is run for BGC detection, we recommend to **not** run Prokka for annotation but instead use the default annotation tool (Pyrodigal) or switch to Prodigal, or (for bacteria only!) Bakta.
 
 ## Databases and reference files
 
@@ -100,7 +100,7 @@ As a reference, we will describe below where and how you can obtain databases an
 
 nf-core/funcscan offers multiple tools for annotating input sequences. Bakta is a new tool touted as a bacteria-only successor to the well-established Prokka.
 
-To supply the preferred Bakta database (and not have the pipeline download at every new run), use the flag `--annotation_bakta_db_localpath`. The full or light Bakta database must be downloaded from the Bakta Zenodo archive, the link of which can be found on the [Bakta GitHub repository](https://github.com/oschwengers/bakta#database-download).
+To supply the preferred Bakta database (and not have the pipeline download it for every new run), use the flag `--annotation_bakta_db_localpath`. The full or light Bakta database must be downloaded from the Bakta Zenodo archive, the link of which can be found on the [Bakta GitHub repository](https://github.com/oschwengers/bakta#database-download).
 
 Once downloaded this must be untarred:
 

nextflow.config

@@ -27,9 +27,9 @@ params {
     annotation_prodigal_forcenonsd          = false
 
     annotation_pyrodigal_singlemode         = false
-    annotation_pyrodigal_closed              = false
-    annotation_pyrodigal_transtable          = 11
-    annotation_pyrodigal_forcenonsd          = false
+    annotation_pyrodigal_closed             = false
+    annotation_pyrodigal_transtable         = 11
+    annotation_pyrodigal_forcenonsd         = false
 
     annotation_bakta_db_localpath           = null
     annotation_bakta_db_downloadtype        = 'full'