Skip to content

Commit

Permalink
Merge pull request #79 from Plant-Food-Research-Open/dev
Browse files Browse the repository at this point in the history
Release candidate for 1.4
  • Loading branch information
GallVp authored Mar 4, 2024
2 parents de1b69f + 5f403db commit 9dfb828
Show file tree
Hide file tree
Showing 354 changed files with 14,339 additions and 11,902 deletions.
28 changes: 28 additions & 0 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,28 @@
{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"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"
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}
20 changes: 15 additions & 5 deletions .editorconfig
Original file line number Diff line number Diff line change
Expand Up @@ -8,19 +8,29 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space

[*.{md,yml,yaml,cff}]
[*.{md,yml,yaml,html,css,scss,js,cff}]
indent_size = 2

[*.nf.test]
insert_final_newline = false

[{LICENSE,LEGAL.txt}]
# 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

[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
[*.{py}]
indent_style = unset

# ignore perl
[*.{pl,pm}]
indent_size = unset
4 changes: 4 additions & 0 deletions .gitattributes
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
6 changes: 6 additions & 0 deletions .github/.dockstore.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
# Dockstore config version, not pipeline version
version: 1.2
workflows:
- subclass: nfl
primaryDescriptorPath: /nextflow.config
publish: True
114 changes: 114 additions & 0 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,114 @@
# plant-food-research-open/assemblyqc: Contributing Guidelines

Hi there!
Many thanks for taking an interest in improving plant-food-research-open/assemblyqc.

We try to manage the required tasks for plant-food-research-open/assemblyqc using GitHub issues, you probably came to this page when creating one.
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 ;)

## Contribution workflow

If you'd like to write some code for plant-food-research-open/assemblyqc, the standard workflow is as follows:

1. Check that there isn't already an issue about your idea in the [plant-food-research-open/assemblyqc issues](https://github.com/plant-food-research-open/assemblyqc/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 [plant-food-research-open/assemblyqc repository](https://github.com/plant-food-research-open/assemblyqc) 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

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/).

## 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>`.

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.

There are typically two types of tests that run:

### Lint tests

`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.

If any failures or warnings are encountered, please follow the listed URL for more documentation.

### Pipeline tests

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.

## Patch

:warning: Only in the unlikely and regretful event of a release happening with a bug.

- 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.

## Pipeline contribution conventions

To make the plant-food-research-open/assemblyqc 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.

### Adding a new step

If you wish to contribute a new step, please use the following coding standards:

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. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.

### Default values

Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope.

Once there, use `nf-core schema build` to add to `nextflow_schema.json`.

### Default processes resource requirements

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.

### Naming schemes

Please use the following naming schemes, to make it easy to understand what is going where.

- initial process channel: `ch_output_from_<process>`
- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`

### Nextflow version bumping

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]`

### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

## GitHub Codespaces

This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.

To get started:

- Open the repo in [Codespaces](https://github.com/plant-food-research-open/assemblyqc/codespaces)
- Tools installed
- nf-core
- Nextflow

Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
54 changes: 54 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,54 @@
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. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud,
or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of plant-food-research-open/assemblyqc _(eg. 1.1, 1.5, 1.8.2)_
"
11 changes: 11 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
name: Feature request
description: Suggest an idea for the plant-food-research-open/assemblyqc 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
25 changes: 25 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
<!--
# plant-food-research-open/assemblyqc pull request
Many thanks for contributing to plant-food-research-open/assemblyqc!
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/plant-food-research-open/assemblyqc/tree/master/.github/CONTRIBUTING.md)
-->

## PR checklist

- [ ] 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/plant-food-research-open/assemblyqc/tree/master/.github/CONTRIBUTING.md)
- [ ] Make sure your code lints (`nf-core lint`) and (`pre-commit run --all`)
- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] 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.
- [ ] `CHANGELOG.md` is updated.
- [ ] `README.md` is updated (including new tool citations and authors/contributors).
44 changes: 44 additions & 0 deletions .github/workflows/branch.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
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]

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 == 'plant-food-research-open/assemblyqc'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name }} == plant-food-research-open/assemblyqc ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
# If the above check failed, post a comment on the PR explaining the failure
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v2
with:
message: |
## This PR is against the `master` branch :x:
* Do not close this PR
* Click _Edit_ and change the `base` to `dev`
* This CI test will remain failed until you push a new commit
---
Hi @${{ 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
43 changes: 43 additions & 0 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,43 @@
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]

env:
NXF_ANSI_LOG: false

concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true

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 == 'plant-food-research-open/assemblyqc') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
RUN_CONFIG:
- "-profile test,docker"
- "-profile docker -c ./tests/stub/stub.config -stub"
- "-profile docker -params-file ./tests/invalid/params.json"
steps:
- name: Check out pipeline code
uses: actions/checkout@v4

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

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} --outdir ./results ${{ matrix.RUN_CONFIG }}
24 changes: 24 additions & 0 deletions .github/workflows/clean-up.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
name: "Close user-tagged issues and PRs"
on:
schedule:
- cron: "0 0 * * 0" # Once a week

jobs:
clean-up:
runs-on: ubuntu-latest
permissions:
issues: write
pull-requests: write
steps:
- uses: actions/stale@v9
with:
stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
days-before-stale: 30
days-before-close: 20
days-before-pr-close: -1
any-of-labels: "awaiting-changes,awaiting-feedback"
exempt-issue-labels: "WIP"
exempt-pr-labels: "WIP"
repo-token: "${{ secrets.GITHUB_TOKEN }}"
Loading

0 comments on commit 9dfb828

Please sign in to comment.