bump dnaapler to v1.0.1

HISTORY.md

@@ -1,6 +1,13 @@
 History
 =======
 
+1.7.4 (2024-11-23)
+------------------
+
+* Adds `--trna_scan_model`  parameter with two accepted options: `--trna_scan_model general` (this will be run by default - what Pharokka has always been running) and `--trna_scan_model bacterial`. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information.
+* Bumps the `dnaapler` dependency to v1.0.1 due to a breaking dependency change in `dnaapler`.
+
+
 1.7.3 (2024-07-10)
 ------------------
 

README.md

@@ -399,6 +399,8 @@ options:
                         extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args "minNR 2 -minRL 21"
   --mash_distance MASH_DISTANCE
                         mash distance for the search against INPHARED. Defaults to 0.2.
+  --trna_scan_model {general,bacterial}
+                        tRNAscan-SE model
   -V, --version         Print pharokka Version
   --citation            Print pharokka Citation
   ```

docs/run.md

@@ -159,6 +159,8 @@ Note 2 things: (1) that you need to leave off the leading hyphen (i.e. `"minNR 2
 pharokka.py -i <fasta file> -o <output folder> -d <path/to/database_dir> -t <threads>  --minced_args "minNR 2 -minRL 21"
 ```
 
+As of v1.7.4 you can specify the bacterial `tRNAscan-SE` model using `--trna_scan_model bacterial`. Otherwise, `pharokka` uses the general model by default. See the [tRNAscan-SE paper](https://doi.org/10.1093/nar/gkab688) for more information.
+
 
 ```bash
 usage: pharokka.py [-h] [-i INFILE] [-o OUTDIR] [-d DATABASE] [-t THREADS] [-f] [-p PREFIX] [-l LOCUSTAG] [-g GENE_PREDICTOR] [-m] [-s]
@@ -217,6 +219,8 @@ options:
                         extra commands to pass to MINced (please omit the leading hyphen for the first argument). You will need to use quotation marks e.g. --minced_args "minNR 2 -minRL 21"
   --mash_distance MASH_DISTANCE
                         mash distance for the search against INPHARED. Defaults to 0.2.
+  --trna_scan_model {general,bacterial}
+                        tRNAscan-SE model
   -V, --version         Print pharokka Version
   --citation            Print pharokka Citation
   ```

environment.yml

@@ -12,7 +12,7 @@ dependencies:
   - minced >=0.4.2
   - aragorn >=1.2.41
   - mash >=2.2
-  - dnaapler >=1.0.0
+  - dnaapler >=1.0.1
   - pyrodigal >=3.1.0
   - pyrodigal-gv >=0.2.0
   - pycirclize >=0.3.1