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Merged
rannick merged 7 commits into from
Apr 3, 2025
Merged

Update Zenodo tag #639

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f27e732
Add missing Zenodo DOI in badge
jfy133 Jan 13, 2025
0ec782c
Fixed HGNC download link
bounlu Mar 25, 2025
5a81c39
Merge branch 'dev' into bounlu-fix-hgnc-link
bounlu Mar 25, 2025
ebabf07
Merge branch 'dev' into bounlu-fix-hgnc-link
rannick Mar 25, 2025
9c14acd
update changelog
rannick Mar 25, 2025
4692a4a
fix spelling
rannick Mar 25, 2025
1fd2f6c
Merge branch 'dev' into bounlu-fix-hgnc-link
rannick Apr 3, 2025
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -23,7 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Add nf-test to local subworkflow: `ARRIBA_WORKFLOW` [#578](https://github.com/nf-core/rnafusion/pull/578)
- Add nf-test to local module: `STARFUSION_BUILD`. [#585](https://github.com/nf-core/rnafusion/pull/585)
- Add nf-test to local module: `STARFUSION_DETECT`. [#586](https://github.com/nf-core/rnafusion/pull/586)
- Added a new module `CTATSPLICING_STARTOCANCERINTRONS` and a new parameter `--ctatsplicing`. This options creates reports on cancer splicing abberations and requires one or both of `--arriba` and `--starfusion` to be given. [#587](https://github.com/nf-core/rnafusion/pull/587)
- Added a new module `CTATSPLICING_STARTOCANCERINTRONS` and a new parameter `--ctatsplicing`. This options creates reports on cancer splicing aberrations and requires one or both of `--arriba` and `--starfusion` to be given. [#587](https://github.com/nf-core/rnafusion/pull/587)
- Add parameter `--references_only` when no data should be analysed, but only the references should be built [#505](https://github.com/nf-core/rnafusion/pull/505)
- Add nf-test to local subworkflow: `FUSIONCATCHER_WORKFLOW` [#591](https://github.com/nf-core/rnafusion/pull/591)
- Add nf-test to local subworkflow: `STARFUSION_WORKFLOW`. [#597](https://github.com/nf-core/rnafusion/pull/597)
Expand All @@ -50,6 +50,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fix error message when parameter outdir is missing [#611](https://github.com/nf-core/rnafusion/pull/611)
- Updated documentation for fusion-report score calculation to reflect 80/20 weight distribution between tool detection and database hits [#620](https://github.com/nf-core/rnafusion/pull/620)
- Update htslib and samtools version in `star/align` to 1.21 [#634](https://github.com/nf-core/rnafusion/pull/634)
- Updated Zenodo DOI in badge [#639](https://github.com/nf-core/rnafusion/pull/639)
- `--run_fusioncatcher` back to `fusioncatcher` [#641](https://github.com/nf-core/rnafusion/pull/641)

### Fixed
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -6,7 +6,7 @@
</h1>

[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/ci.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2565517-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2565517)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
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