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Important! Template update for nf-core/tools v2.14.1 #91

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merged 7 commits into from
May 10, 2024
Merged

Important! Template update for nf-core/tools v2.14.1 #91

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e83eacc
Template update for nf-core/tools version 2.14.1
nf-core-bot May 9, 2024
fec0fcb
Merge branch 'dev' into nf-core-template-merge-2.14.1
maxulysse May 10, 2024
4920f9b
[automated] Fix code linting
nf-core-bot May 10, 2024
eca1593
fix DOI
maxulysse May 10, 2024
517d9d9
fix linting
maxulysse May 10, 2024
0381ee2
fix linting
maxulysse May 10, 2024
1d872ef
Update CHANGELOG.md
maxulysse May 10, 2024
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7 changes: 5 additions & 2 deletions .github/CONTRIBUTING.md
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Expand Up @@ -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 <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
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No sure that works for bamtofastq but let me try.

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$ nf-test test --profile debug,test,docker --verbose

🚀 nf-test 0.8.4
https://code.askimed.com/nf-test
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr

Warning: This pipeline has no nf-test config file.
Error: No tests or test directories containing scripts that end with *.test provided.

```

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.
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3 changes: 2 additions & 1 deletion .github/workflows/download_pipeline.yml
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Expand Up @@ -82,4 +82,5 @@ jobs:
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
1 change: 0 additions & 1 deletion .github/workflows/linting.yml
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Expand Up @@ -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
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5 changes: 1 addition & 4 deletions .nf-core.yml
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@@ -1,5 +1,2 @@
repository_type: pipeline
nf_core_version: "2.14.0"
lint:
files_unchanged:
- .github/CONTRIBUTING.md
nf_core_version: "2.14.1"
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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
- [#91](https://github.com/nf-core/bamtofastq/pull/91) - Sync TEMPLATE with tools 2.14.1

### `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/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/)
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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
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