From e83eacca5066176ccaae148b306a1ab062b95566 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 9 May 2024 11:37:51 +0000 Subject: [PATCH 1/6] Template update for nf-core/tools version 2.14.1 --- .github/workflows/linting.yml | 1 - .nf-core.yml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a3fb254..1fcafe8 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -20,7 +20,6 @@ jobs: uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 with: python-version: "3.12" - cache: "pip" - name: Install pre-commit run: pip install pre-commit diff --git a/.nf-core.yml b/.nf-core.yml index d6daa40..e0b85a7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,2 @@ repository_type: pipeline -nf_core_version: "2.14.0" +nf_core_version: "2.14.1" From 4920f9ba687e4ed12b237b400b7a0e15b67ab167 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 10 May 2024 12:16:02 +0000 Subject: [PATCH 2/6] [automated] Fix code linting --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 712ad3a..c6a8d05 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -82,4 +82,4 @@ jobs: if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: NXF_SINGULARITY_CACHEDIR: ./ - NXF_SINGULARITY_HOME_MOUNT: true \ No newline at end of file + NXF_SINGULARITY_HOME_MOUNT: true From eca159397113f6cf563270739358671d6f463f10 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 10 May 2024 14:48:47 +0200 Subject: [PATCH 3/6] fix DOI --- README.md | 2 +- nextflow.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index b5e9c56..a6f7003 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![GitHub Actions CI Status](https://github.com/nf-core/bamtofastq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/bamtofastq/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/bamtofastq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/bamtofastq/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/bamtofastq/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/bamtofastq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/bamtofastq/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/bamtofastq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.4710628-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.4710628) [![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%A523.04.0-23aa62.svg)](https://www.nextflow.io/) diff --git a/nextflow.config b/nextflow.config index fd59ded..835e6e1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -254,7 +254,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' version = '2.1.2dev' - doi = 'https://doi.org/10.5281/zenodo.4710628' + doi = '10.5281/zenodo.4710628' } // Load modules.config for DSL2 module specific options From 517d9d9892836fc868b8f8c93e7049c6c1960404 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 10 May 2024 14:50:57 +0200 Subject: [PATCH 4/6] fix linting --- .nf-core.yml | 3 --- CHANGELOG.md | 1 + 2 files changed, 1 insertion(+), 3 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index ac969c6..e0b85a7 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,5 +1,2 @@ repository_type: pipeline nf_core_version: "2.14.1" -lint: - files_unchanged: - - .github/CONTRIBUTING.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 9b26570..a1dea4e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - [#90](https://github.com/nf-core/bamtofastq/pull/90) - Sync TEMPLATE with tools 2.14.0 +- [#90](https://github.com/nf-core/bamtofastq/pull/90) - Sync TEMPLATE with tools 2.14.1 ### `Fixed` From 0381ee2fa18c0cf2d0fe41c767cecb53e6ad8df1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 10 May 2024 14:53:54 +0200 Subject: [PATCH 5/6] fix linting --- .github/CONTRIBUTING.md | 7 +++++-- .github/workflows/download_pipeline.yml | 1 + 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 49c279a..e49d88a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -26,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests -You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to -receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. +You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: + +```bash +nf-test test --profile debug,test,docker --verbose +``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index c6a8d05..2d20d64 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -83,3 +83,4 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./ NXF_SINGULARITY_HOME_MOUNT: true + run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results From 1d872efd7a43115e809882087c51311a7e2c1865 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 10 May 2024 15:11:43 +0200 Subject: [PATCH 6/6] Update CHANGELOG.md Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a1dea4e..dc0fb74 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Changed` - [#90](https://github.com/nf-core/bamtofastq/pull/90) - Sync TEMPLATE with tools 2.14.0 -- [#90](https://github.com/nf-core/bamtofastq/pull/90) - Sync TEMPLATE with tools 2.14.1 +- [#91](https://github.com/nf-core/bamtofastq/pull/91) - Sync TEMPLATE with tools 2.14.1 ### `Fixed`