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feat: Strict syntax compatibility to enable better error reporting #30

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Merged
fellen31 merged 8 commits into from
Mar 5, 2026
+24 −12
Merged

feat: Strict syntax compatibility to enable better error reporting #30

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6c4e0a6
Strict syntax enables better error reporting
fellen31 Mar 4, 2026
426b0fe
since readme has been updated
fellen31 Mar 4, 2026
9382a36
update changelog
fellen31 Mar 4, 2026
81c1971
use the correct min nextflow version
fellen31 Mar 4, 2026
3b47496
no fix needed
fellen31 Mar 4, 2026
90a0402
Merge branch 'dev' into 29-strict-syntax-compatability
fellen31 Mar 5, 2026
17c5efe
Should be under changed
fellen31 Mar 5, 2026
9631928
Changing the minimum Nextflow version should also have a changelog entry
fellen31 Mar 5, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/nf-test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ jobs:
- isMain: false
profile: "singularity"
NXF_VER:
- "25.04.0"
- "25.10.0"
- "latest-everything"
env:
NXF_ANSI_LOG: false
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -16,10 +16,13 @@ Initial release of nf-core/oncorefiner, created with the [nf-core](https://nf-co
- Added filtering for SV vcf file [#5](https://github.com/Clinical-Genomics/oncorefiner/pull/5)
- Added small test profile. The related test dataset have been added as a branch called oncorefiner under [Clinical-Genomics/test-datasets](https://github.com/Clinical-Genomics/test-datasets/tree/oncorefiner) [#8](https://github.com/Clinical-Genomics/oncorefiner/pull/8)
- Added CI checks for `Conventional PR title`, `Updated changelog` and `Add PR checklist comment` [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18)
- Added Nextflow strict syntax compatibility [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30)

### Changed

- Updated PR template, PR checklist, feature request template, bug report template and issue template chooser [#24](https://github.com/Clinical-Genomics/oncorefiner/pull/24)
- Updated nf-schema to 2.6.1 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30)
- Updated minimum Nextflow version to 25.10.0 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30)

### `Fixed`

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -10,7 +10,7 @@
[![GitHub Actions Linting Status](https://github.com/nf-core/oncorefiner/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/oncorefiner/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/oncorefiner/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -271,14 +271,14 @@ manifest {
description = """Customizable post-processing and extension layer built on top of Oncoanalyser that adapts its outputs to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser robust core"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.04.0'
nextflowVersion = '!>=25.10.0'
version = '1.0.0dev'
doi = ''
}

// Nextflow plugins
plugins {
id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-schema@2.6.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}

validation {
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