Version bump, changelog, contribution metadata

.github/workflows/linting.yml

@@ -53,15 +53,15 @@ jobs:
           pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.nf-core.yml

@@ -43,4 +43,4 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 0.7.1
+  version: 0.8.0

CHANGELOG.md

@@ -3,6 +3,33 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[0.8.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.8.0)] – Sprigatito – [2025-05-19]
+
+### Enhancements & fixes
+
+- Runtime of the blast commands is now capped at 12 hours (#166)
+- Upgraded Busco and added an option to control the gene predictor used (#160, #174, #181)
+- nf-core template upgrade (to version 3.2.1) (#164, #176)
+- Documentation fixes (broken links) (#175)
+- Ability to run without any read data (#177)
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| blobtoolkit | 4.4.4       | 4.4.6       |
+| busco       | 5.7.1       | 5.8.3       |
+
+### Parameters
+
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+|               | --busco_gene_predictor |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
 ## [[0.7.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.7.1)] – Psyduck (patch 1) – [2025-03-29]
 
 ### Enhancements & fixes

CITATION.cff

@@ -1,48 +1,69 @@
-cff-version: 1.2.0
-title: sanger-tol/blobtoolkit v0.7.1
 authors:
-  - family-names: Butt
+  - affiliation: Wellcome Sanger Institute
+    family-names: Butt
     given-names: Zaynab
-    affiliation: Wellcome Sanger Institute
-    orcid: 0009-0009-7934-8440
-  - family-names: Chafin
+    orcid: https://orcid.org/0009-0009-7934-8440
+    website: https://github.com/zb32
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Chafin
     given-names: Tyler
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0001-8687-5905
-  - family-names: Challis
+    orcid: https://orcid.org/0000-0001-8687-5905
+    website: https://github.com/tkchafin
+  - affiliation: Wellcome Sanger Institute
+    family-names: Challis
     given-names: Rich
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0002-3502-1122
-  - family-names: Kumar
+    orcid: https://orcid.org/0000-0002-3502-1122
+    website: https://github.com/rjchallis
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Kumar
     given-names: Sujai
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0001-5902-6641
-  - family-names: Muffato
+    orcid: https://orcid.org/0000-0001-5902-6641
+    website: https://github.com/sujaikumar
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Muffato
     given-names: Matthieu
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0002-7860-3560
-  - family-names: Pointon
-    given-names: Damon-Lee
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0003-2949-6719
-  - family-names: Qi
+    orcid: https://orcid.org/0000-0002-7860-3560
+    website: https://github.com/muffato
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Qi
     given-names: Guoying
-    orcid: 0000-0003-1262-8973
-    affiliation: Wellcome Sanger Institute
-  - family-names: "Ramos D\xEDaz"
+    orcid: https://orcid.org/0000-0003-1262-8973
+    website: https://github.com/gq1
+  - email: [email protected]
+    family-names: "Ramos D\xEDaz"
     given-names: Alexander
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0001-6410-3349
-  - family-names: Surana
+    orcid: https://orcid.org/0000-0001-6410-3349
+    website: https://github.com/alxndrdiaz
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Sims
+    given-names: Yumi
+    orcid: https://orcid.org/0000-0003-4765-4872
+    website: https://github.com/yumisims
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Surana
     given-names: Priyanka
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0002-7167-0875
-  - family-names: Yates
+    orcid: https://orcid.org/0000-0002-7167-0875
+    website: https://github.com/priyanka-surana
+  - affiliation: Wellcome Sanger Institute
+    email: [email protected]
+    family-names: Yates
     given-names: Bethan
-    affiliation: Wellcome Sanger Institute
-    orcid: 0000-0003-1658-1762
-doi: 10.5281/zenodo.13758882
-repository-code: "https://github.com/sanger-tol/blobtoolkit"
+    orcid: https://orcid.org/0000-0003-1658-1762
+    website: https://github.com/BethYates
+cff-version: 1.2.0
+date-released: "2025-04-25"
+doi: 10.5281/zenodo.7949058
 license: MIT
-version: 0.7.1
-date-released: "2024-09-13"
+message: If you use this software, please cite it using the metadata from this file
+  and all references from CITATIONS.md .
+repository-code: https://github.com/sanger-tol/blobtoolkit
+title: sanger-tol/blobtoolkit v0.8.0 -
+type: software
+url: https://pipelines.tol.sanger.ac.uk/blobtoolkit
+version: 0.8.0

docs/usage.md

@@ -52,6 +52,22 @@ An [example samplesheet](../assets/test/samplesheet.csv) has been provided with
 The pipeline can also accept a samplesheet generated by the [nf-core/fetchngs](https://nf-co.re/fetchngs) pipeline (tested with version 1.11.0).
 The pipeline then needs the `--fetchngs_samplesheet true` option _and_ `--align true`, since the data files would all be unaligned.
 
+## BUSCO
+
+BUSCO is an important part of the assessment done by the pipeline.
+
+### Gene prediction method
+
+Busco starts with a quick gene prediction run, for which it has the following options (by decreasing speed):
+
+- Miniprot
+- Metaeuk
+- Augustus
+
+The default value has changed across Busco versions (and may change in the future).
+The pipeline exposes the `--busco_gene_predictor` option to force a specific method to be used.
+Otherwise, the pipeline will default to Busco's own default (currently Miniprot).
+
 ### Support for pre-computed `BUSCO` outputs
 
 The pipeline may be optionally run with a set of pre-computed [`BUSCO`](https://busco.ezlab.org) runs, provided using the `--precomputed_busco` parameter. These can be provided as either a directory path, or a `.tar.gz` compressed archive. The contents should be each `run_` output directory (directly from `BUSCO`) named as `run_[odb_dabasase_name]`:

nextflow.config

@@ -279,7 +279,7 @@ manifest {
             affiliation: 'Wellcome Sanger Institute',
             github: 'https://github.com/rjchallis',
             contribution: ['author'],
-            orcid: 'https://orcid.org/0000-0002-3502-112'
+            orcid: 'https://orcid.org/0000-0002-3502-1122'
         ],
         [
             name: 'Kumar, Sujai',
@@ -308,6 +308,13 @@ manifest {
             contribution: ['author'],
             orcid: 'https://orcid.org/0000-0001-6410-3349'
         ],
+        [
+            name: 'Sims, Yumi',
+            affiliation: 'Wellcome Sanger Institute',
+            github: 'https://github.com/yumisims',
+            contribution: ['contributor'],
+            orcid: 'https://orcid.org/0000-0003-4765-4872'
+        ],
         [
             name: 'Surana, Priyanka',
             affiliation: 'Wellcome Sanger Institute',
@@ -328,7 +335,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=24.04.2'
-    version         = '0.7.1'
+    version         = '0.8.0'
     doi             = '10.5281/zenodo.7949058'
 }