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Important! Template update for nf-core/tools v2.14.1 #242

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Template update for nf-core/tools version 2.13.1
nf-core-bot committed Feb 29, 2024

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This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
commit 5d928b83fbecc36e81016fa778c8ffcf4b71bd44
10 changes: 1 addition & 9 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -10,15 +10,7 @@
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},

// Add the IDs of extensions you want installed when the container is created.
14 changes: 8 additions & 6 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -9,9 +9,8 @@ Please use the pre-filled template to save time.
However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)

:::info
If you need help using or modifying nf-core/cutandrun then the best place to ask is on the nf-core Slack [#cutandrun](https://nfcore.slack.com/channels/cutandrun) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::
> [!NOTE]
> If you need help using or modifying nf-core/cutandrun then the best place to ask is on the nf-core Slack [#cutandrun](https://nfcore.slack.com/channels/cutandrun) channel ([join our Slack here](https://nf-co.re/join/slack)).

## Contribution workflow

@@ -27,8 +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
```

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.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.

### Naming schemes

2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cuta
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/cutandrun/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/cutandrun _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
- [ ] Output Documentation in `docs/output.md` is updated.
4 changes: 2 additions & 2 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
@@ -14,7 +14,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
# Add full size test data (but still relatively small datasets for few samples)
# on the `test_full.config` test runs with only one set of parameters
@@ -31,7 +31,7 @@ jobs:
}
profiles: test_full

- uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
path: |
4 changes: 2 additions & 2 deletions .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@ jobs:
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,7 +25,7 @@ jobs:
}
profiles: test

- uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
path: |
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -31,7 +31,7 @@ jobs:
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

2 changes: 1 addition & 1 deletion .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
@@ -28,7 +28,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
Original file line number Diff line number Diff line change
@@ -35,7 +35,7 @@ jobs:
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
uses: nf-core/setup-nextflow@v1

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
2 changes: 1 addition & 1 deletion .github/workflows/release-announcements.yml
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@ jobs:
- name: get topics and convert to hashtags
id: get_topics
run: |
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT

- uses: rzr/fediverse-action@master
with:
6 changes: 2 additions & 4 deletions .gitpod.yml
Original file line number Diff line number Diff line change
@@ -10,13 +10,11 @@ tasks:

vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code
- charliermarsh.ruff # Code linter Ruff
3 changes: 2 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -7,12 +7,13 @@

[![GitHub Actions CI Status](https://github.com/nf-core/cutandrun/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/cutandrun/actions/workflows/ci.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/cutandrun/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/cutandrun/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/cutandrun/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/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
[![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/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/cutandrun)
[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/cutandrun)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23cutandrun-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/cutandrun)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)

8 changes: 4 additions & 4 deletions modules.json
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@
},
"multiqc": {
"branch": "master",
"git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
"git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
"installed_by": ["modules"]
}
}
@@ -21,17 +21,17 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "262b17ed2aad591039f914951659177e6c39a8d8",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
"branch": "master",
"git_sha": "cd08c91373cd00a73255081340e4914485846ba1",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"installed_by": ["subworkflows"]
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/multiqc/environment.yml

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4 changes: 2 additions & 2 deletions modules/nf-core/multiqc/main.nf

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12 changes: 6 additions & 6 deletions modules/nf-core/multiqc/tests/main.nf.test.snap

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10 changes: 7 additions & 3 deletions subworkflows/local/utils_nfcore_cutandrun_pipeline/main.nf
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
//
// Subworkflow with functionality specific to the nf-core/pipeline pipeline
// Subworkflow with functionality specific to the nf-core/cutandrun pipeline
//

/*
@@ -152,7 +152,9 @@ workflow PIPELINE_COMPLETION {
//
def validateInputParameters() {
genomeExistsError()
}//
}

//
// Validate channels from input samplesheet
//
def validateInputSamplesheet(input) {
@@ -190,7 +192,9 @@ def genomeExistsError() {
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
error(error_string)
}
}//
}

//
// Generate methods description for MultiQC
//
def toolCitationText() {

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.