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initial template build from nf-core/tools, version 2.5.dev0
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root = true | ||
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[*] | ||
charset = utf-8 | ||
end_of_line = lf | ||
insert_final_newline = true | ||
trim_trailing_whitespace = true | ||
indent_size = 4 | ||
indent_style = space | ||
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[*.{md,yml,yaml,html,css,scss,js,cff}] | ||
indent_size = 2 | ||
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# These files are edited and tested upstream in nf-core/modules | ||
[/modules/nf-core/**] | ||
charset = unset | ||
end_of_line = unset | ||
insert_final_newline = unset | ||
trim_trailing_whitespace = unset | ||
indent_style = unset | ||
indent_size = unset | ||
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[/assets/email*] | ||
indent_size = unset |
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*.config linguist-language=nextflow | ||
modules/nf-core/** linguist-generated | ||
subworkflows/nf-core/** linguist-generated |
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# Dockstore config version, not pipeline version | ||
version: 1.2 | ||
workflows: | ||
- subclass: nfl | ||
primaryDescriptorPath: /nextflow.config | ||
publish: True |
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# sanger-tol/genomeassembly: Contributing Guidelines | ||
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Hi there! | ||
Many thanks for taking an interest in improving sanger-tol/genomeassembly. | ||
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We try to manage the required tasks for sanger-tol/genomeassembly using GitHub issues, you probably came to this page when creating one. | ||
Please use the pre-filled template to save time. | ||
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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 ;) | ||
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## Contribution workflow | ||
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If you'd like to write some code for sanger-tol/genomeassembly, the standard workflow is as follows: | ||
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1. Check that there isn't already an issue about your idea in the [sanger-tol/genomeassembly issues](https://github.com/sanger-tol/genomeassembly/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this | ||
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [sanger-tol/genomeassembly repository](https://github.com/sanger-tol/genomeassembly) to your GitHub account | ||
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) | ||
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). | ||
5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged | ||
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If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). | ||
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## Tests | ||
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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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There are typically two types of tests that run: | ||
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### Lint tests | ||
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`nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. | ||
To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint <pipeline-directory>` command. | ||
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If any failures or warnings are encountered, please follow the listed URL for more documentation. | ||
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### Pipeline tests | ||
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Each `nf-core` pipeline should be set up with a minimal set of test-data. | ||
`GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. | ||
If there are any failures then the automated tests fail. | ||
These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. | ||
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## Patch | ||
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:warning: Only in the unlikely and regretful event of a release happening with a bug. | ||
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- On your own fork, make a new branch `patch` based on `upstream/master`. | ||
- Fix the bug, and bump version (X.Y.Z+1). | ||
- A PR should be made on `master` from patch to directly this particular bug. | ||
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## Pipeline contribution conventions | ||
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To make the sanger-tol/genomeassembly code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. | ||
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### Adding a new step | ||
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If you wish to contribute a new step, please use the following coding standards: | ||
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1. Define the corresponding input channel into your new process from the expected previous process channel | ||
2. Write the process block (see below). | ||
3. Define the output channel if needed (see below). | ||
4. Add any new parameters to `nextflow.config` with a default (see below). | ||
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). | ||
6. Add sanity checks and validation for all relevant parameters. | ||
7. Perform local tests to validate that the new code works as expected. | ||
8. If applicable, add a new test command in `.github/workflow/ci.yml`. | ||
9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. | ||
10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. | ||
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### Default values | ||
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Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. | ||
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Once there, use `nf-core schema build` to add to `nextflow_schema.json`. | ||
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### Default processes resource requirements | ||
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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. | ||
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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. | ||
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### Naming schemes | ||
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Please use the following naming schemes, to make it easy to understand what is going where. | ||
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- initial process channel: `ch_output_from_<process>` | ||
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>` | ||
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### Nextflow version bumping | ||
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If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` | ||
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### Images and figures | ||
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For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). |
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name: Bug report | ||
description: Report something that is broken or incorrect | ||
labels: bug | ||
body: | ||
- type: textarea | ||
id: description | ||
attributes: | ||
label: Description of the bug | ||
description: A clear and concise description of what the bug is. | ||
validations: | ||
required: true | ||
- type: textarea | ||
id: command_used | ||
attributes: | ||
label: Command used and terminal output | ||
description: Steps to reproduce the behaviour. Please paste the command you used | ||
to launch the pipeline and the output from your terminal. | ||
render: console | ||
placeholder: "$ nextflow run ... | ||
Some output where something broke | ||
" | ||
- type: textarea | ||
id: files | ||
attributes: | ||
label: Relevant files | ||
description: "Please drag and drop the relevant files here. Create a `.zip` archive | ||
if the extension is not allowed. | ||
Your verbose log file `.nextflow.log` is often useful _(this is a hidden file | ||
in the directory where you launched the pipeline)_ as well as custom Nextflow | ||
configuration files. | ||
" | ||
- type: textarea | ||
id: system | ||
attributes: | ||
label: System information | ||
description: "* Nextflow version _(eg. 21.10.3)_ | ||
* Hardware _(eg. HPC, Desktop, Cloud)_ | ||
* Executor _(eg. slurm, local, awsbatch)_ | ||
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ | ||
* OS _(eg. CentOS Linux, macOS, Linux Mint)_ | ||
* Version of sanger-tol/genomeassembly _(eg. 1.1, 1.5, 1.8.2)_ | ||
" |
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name: Feature request | ||
description: Suggest an idea for the sanger-tol/genomeassembly pipeline | ||
labels: enhancement | ||
body: | ||
- type: textarea | ||
id: description | ||
attributes: | ||
label: Description of feature | ||
description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. | ||
validations: | ||
required: true |
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<!-- | ||
# sanger-tol/genomeassembly pull request | ||
Many thanks for contributing to sanger-tol/genomeassembly! | ||
Please fill in the appropriate checklist below (delete whatever is not relevant). | ||
These are the most common things requested on pull requests (PRs). | ||
Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. | ||
Learn more about contributing: [CONTRIBUTING.md](https://github.com/sanger-tol/genomeassembly/tree/master/.github/CONTRIBUTING.md) | ||
--> | ||
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## PR checklist | ||
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- [ ] This comment contains a description of changes (with reason). | ||
- [ ] If you've fixed a bug or added code that should be tested, add tests! | ||
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/sanger-tol/genomeassembly/tree/master/.github/CONTRIBUTING.md) | ||
- [ ] Make sure your code lints (`nf-core lint`). | ||
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`). | ||
- [ ] Usage Documentation in `docs/usage.md` is updated. | ||
- [ ] Output Documentation in `docs/output.md` is updated. | ||
- [ ] `CHANGELOG.md` is updated. | ||
- [ ] `README.md` is updated (including new tool citations and authors/contributors). |
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name: nf-core branch protection | ||
# This workflow is triggered on PRs to master branch on the repository | ||
# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` | ||
on: | ||
pull_request_target: | ||
branches: [master] | ||
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jobs: | ||
test: | ||
runs-on: ubuntu-latest | ||
steps: | ||
# PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches | ||
- name: Check PRs | ||
if: github.repository == 'sanger-tol/genomeassembly' | ||
run: | | ||
{ [[ ${{github.event.pull_request.head.repo.full_name }} == sanger-tol/genomeassembly ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] | ||
# If the above check failed, post a comment on the PR explaining the failure | ||
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets | ||
- name: Post PR comment | ||
if: failure() | ||
uses: mshick/add-pr-comment@v1 | ||
with: | ||
message: | | ||
## This PR is against the `master` branch :x: | ||
* Do not close this PR | ||
* Click _Edit_ and change the `base` to `dev` | ||
* This CI test will remain failed until you push a new commit | ||
--- | ||
Hi @${{ github.event.pull_request.user.login }}, | ||
It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. | ||
The `master` branch on nf-core repositories should always contain code from the latest release. | ||
Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. | ||
You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. | ||
Note that even after this, the test will continue to show as failing until you push a new commit. | ||
Thanks again for your contribution! | ||
repo-token: ${{ secrets.GITHUB_TOKEN }} | ||
allow-repeats: false |
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name: nf-core CI | ||
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
on: | ||
push: | ||
branches: | ||
- dev | ||
pull_request: | ||
release: | ||
types: [published] | ||
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env: | ||
NXF_ANSI_LOG: false | ||
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jobs: | ||
test: | ||
name: Run pipeline with test data | ||
# Only run on push if this is the nf-core dev branch (merged PRs) | ||
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'sanger-tol/genomeassembly') }}" | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
NXF_VER: | ||
- "21.10.3" | ||
- "latest-everything" | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v2 | ||
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- name: Install Nextflow | ||
uses: nf-core/setup-nextflow@v1 | ||
with: | ||
version: "${{ matrix.NXF_VER }}" | ||
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- name: Run pipeline with test data | ||
# TODO nf-core: You can customise CI pipeline run tests as required | ||
# For example: adding multiple test runs with different parameters | ||
# Remember that you can parallelise this by using strategy.matrix | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results |
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name: Fix linting from a comment | ||
on: | ||
issue_comment: | ||
types: [created] | ||
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jobs: | ||
deploy: | ||
# Only run if comment is on a PR with the main repo, and if it contains the magic keywords | ||
if: > | ||
contains(github.event.comment.html_url, '/pull/') && | ||
contains(github.event.comment.body, '@nf-core-bot fix linting') && | ||
github.repository == 'sanger-tol/genomeassembly' | ||
runs-on: ubuntu-latest | ||
steps: | ||
# Use the @nf-core-bot token to check out so we can push later | ||
- uses: actions/checkout@v3 | ||
with: | ||
token: ${{ secrets.nf_core_bot_auth_token }} | ||
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# Action runs on the issue comment, so we don't get the PR by default | ||
# Use the gh cli to check out the PR | ||
- name: Checkout Pull Request | ||
run: gh pr checkout ${{ github.event.issue.number }} | ||
env: | ||
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} | ||
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- uses: actions/setup-node@v2 | ||
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- name: Install Prettier | ||
run: npm install -g prettier @prettier/plugin-php | ||
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# Check that we actually need to fix something | ||
- name: Run 'prettier --check' | ||
id: prettier_status | ||
run: | | ||
if prettier --check ${GITHUB_WORKSPACE}; then | ||
echo "::set-output name=result::pass" | ||
else | ||
echo "::set-output name=result::fail" | ||
fi | ||
- name: Run 'prettier --write' | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: prettier --write ${GITHUB_WORKSPACE} | ||
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- name: Commit & push changes | ||
if: steps.prettier_status.outputs.result == 'fail' | ||
run: | | ||
git config user.email "[email protected]" | ||
git config user.name "nf-core-bot" | ||
git config push.default upstream | ||
git add . | ||
git status | ||
git commit -m "[automated] Fix linting with Prettier" | ||
git push |
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