From 5b0fd9357fd9e6a8ad63110ea36c6ce080973122 Mon Sep 17 00:00:00 2001 From: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com> Date: Mon, 1 Jul 2024 19:29:29 +0000 Subject: [PATCH] FEAT: update busco to 5.7.1 --- CHANGELOG.md | 4 ++++ src/busco/busco_download_datasets/config.vsh.yaml | 2 +- src/busco/busco_list_datasets/config.vsh.yaml | 2 +- src/busco/busco_run/config.vsh.yaml | 6 +++++- src/busco/busco_run/help.txt | 9 ++++++--- src/busco/busco_run/script.sh | 1 + 6 files changed, 18 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b5c403af..3a036fba 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/src/busco/busco_download_datasets/config.vsh.yaml b/src/busco/busco_download_datasets/config.vsh.yaml index 04d76dd6..5297af2e 100644 --- a/src/busco/busco_download_datasets/config.vsh.yaml +++ b/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: | diff --git a/src/busco/busco_list_datasets/config.vsh.yaml b/src/busco/busco_list_datasets/config.vsh.yaml index 6ada7c84..cac34cc6 100644 --- a/src/busco/busco_list_datasets/config.vsh.yaml +++ b/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: | diff --git a/src/busco/busco_run/config.vsh.yaml b/src/busco/busco_run/config.vsh.yaml index d79f03f5..23ee95fb 100644 --- a/src/busco/busco_run/config.vsh.yaml +++ b/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: | diff --git a/src/busco/busco_run/help.txt b/src/busco/busco_run/help.txt index 2cacec4d..6d83f9be 100644 --- a/src/busco/busco_run/help.txt +++ b/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. diff --git a/src/busco/busco_run/script.sh b/src/busco/busco_run/script.sh index 5b562f83..fd493e7b 100644 --- a/src/busco/busco_run/script.sh +++ b/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} \