FEAT: update busco to 5.7.1

CHANGELOG.md

@@ -8,6 +8,10 @@
 
 * `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
 
+## MINOR CHANGES
+
+* `busco` components: update BUSCO to `5.7.1`.
+
 # biobox 0.1.0
 
 ## BREAKING CHANGES

src/busco/busco_download_datasets/config.vsh.yaml

@@ -37,7 +37,7 @@ test_resources:
     path: test.sh
 engines:
   - type: docker
-    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |

src/busco/busco_list_datasets/config.vsh.yaml

@@ -29,7 +29,7 @@ test_resources:
     path: test.sh
 engines:
   - type: docker
-    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |

src/busco/busco_run/config.vsh.yaml

@@ -181,6 +181,10 @@ argument_groups:
 
   - name: MetaEuk Settings
     arguments:
+      - name: --metaeuk
+        type: boolean_true
+        description: |
+          Use Metaeuk gene predictor.
       - name: --metaeuk_parameters
         type: string
         description: |
@@ -204,7 +208,7 @@ test_resources:
     path: test_data
 engines:
   - type: docker
-    image: quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0
+    image: quay.io/biocontainers/busco:5.7.1--pyhdfd78af_0
     setup:
       - type: docker
         run: |

src/busco/busco_run/help.txt

@@ -2,7 +2,9 @@
 busco -h
 ```
 
-Welcome to BUSCO 5.6.1: the Benchmarking Universal Single-Copy Ortholog assessment tool.
+usage: busco -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
+
+Welcome to BUSCO 5.7.1: the Benchmarking Universal Single-Copy Ortholog assessment tool.
 For more detailed usage information, please review the README file provided with this distribution and the BUSCO user guide. Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
 
 optional arguments:
@@ -18,7 +20,7 @@ optional arguments:
   -l LINEAGE, --lineage_dataset LINEAGE
                         Specify the name of the BUSCO lineage to be used.
   --augustus            Use augustus gene predictor for eukaryote runs
-  --augustus_parameters --PARAM1=VALUE1,--PARAM2=VALUE2
+  --augustus_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
                         Pass additional arguments to Augustus. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
   --augustus_species AUGUSTUS_SPECIES
                         Specify a species for Augustus training.
@@ -42,11 +44,12 @@ optional arguments:
   --limit N             How many candidate regions (contig or transcript) to consider per BUSCO (default: 3)
   --list-datasets       Print the list of available BUSCO datasets
   --long                Optimization Augustus self-training mode (Default: Off); adds considerably to the run time, but can improve results for some non-model organisms
+  --metaeuk             Use Metaeuk gene predictor
   --metaeuk_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
                         Pass additional arguments to Metaeuk for the first run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
   --metaeuk_rerun_parameters "--PARAM1=VALUE1,--PARAM2=VALUE2"
                         Pass additional arguments to Metaeuk for the second run. All arguments should be contained within a single string with no white space, with each argument separated by a comma.
-  --miniprot            Use miniprot gene predictor
+  --miniprot            Use Miniprot gene predictor
   --skip_bbtools        Skip BBTools for assembly statistics
   --offline             To indicate that BUSCO cannot attempt to download files
   --opt-out-run-stats   Opt out of data collection. Information on the data collected is available in the user guide.

src/busco/busco_run/script.sh

@@ -39,6 +39,7 @@ busco \
     ${par_force:+--force} \
     ${par_limit:+--limit "$par_limit"} \
     ${par_long:+--long} \
+    ${pat_metaeuk:+--metaeuk} \
     ${par_metaeuk_parameters:+--metaeuk_parameters "$par_metaeuk_parameters"} \
     ${par_metaeuk_rerun_parameters:+--metaeuk_rerun_parameters "$par_metaeuk_rerun_parameters"} \
     ${par_miniprot:+--miniprot} \