Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Important! Template update for nf-core/tools v3.1.0 #37

Closed
wants to merge 4 commits into from
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 12 additions & 12 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# nf-core/callingcards: Contributing Guidelines
# `nf-core/callingcards`: Contributing Guidelines

Hi there!
Many thanks for taking an interest in improving nf-core/callingcards.
Expand All @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/callingcards, the standard workflow
1. Check that there isn't already an issue about your idea in the [nf-core/callingcards issues](https://github.com/nf-core/callingcards/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 [nf-core/callingcards repository](https://github.com/nf-core/callingcards) 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).
4. Use `nf-core pipelines 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/).
Expand All @@ -40,7 +40,7 @@ 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.
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 pipelines lint <pipeline-directory>` command.

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

Expand All @@ -55,27 +55,27 @@ These tests are run both with the latest available version of `Nextflow` and als

: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`.
- On your own fork, make a new branch `patch` based on `upstream/main` or `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.
- Open a pull-request from `patch` to `main`/`master` with the changes.

## Getting help

For further information/help, please consult the [nf-core/callingcards documentation](https://nf-co.re/callingcards/usage) and don't hesitate to get in touch on the nf-core Slack [#callingcards](https://nfcore.slack.com/channels/callingcards) channel ([join our Slack here](https://nf-co.re/join/slack)).

## Pipeline contribution conventions

To make the nf-core/callingcards 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.
To make the `nf-core/callingcards` 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
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).
5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines 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`.
Expand All @@ -84,13 +84,13 @@ If you wish to contribute a new step, please use the following coding standards:

### Default values

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

Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
Once there, use `nf-core pipelines 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.
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/main/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 `${task.cpus}` and `${task.memory}` variables in the `script:` block.

Expand All @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g

### 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]`
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 pipelines bump-version --nextflow . [min-nf-version]`

### Images and figures

Expand Down
2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/call
- [ ] 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/nf-core/callingcards/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/callingcards _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] Make sure your code lints (`nf-core lint`).
- [ ] Make sure your code lints (`nf-core pipelines lint`).
- [ ] 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.
Expand Down
38 changes: 34 additions & 4 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
@@ -1,18 +1,48 @@
name: nf-core AWS full size tests
# This workflow is triggered on published releases.
# This workflow is triggered on PRs opened against the main/master branch.
# It can be additionally triggered manually with GitHub actions workflow dispatch button.
# It runs the -profile 'test_full' on AWS batch

on:
release:
types: [published]
pull_request:
branches:
- main
- master
workflow_dispatch:
pull_request_review:
types: [submitted]

jobs:
run-platform:
name: Run AWS full tests
if: github.repository == 'nf-core/callingcards'
# run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
if: github.repository == 'nf-core/callingcards' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
runs-on: ubuntu-latest
steps:
- name: Get PR reviews
uses: octokit/[email protected]
if: github.event_name != 'workflow_dispatch'
id: check_approvals
continue-on-error: true
with:
route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

- name: Check for approvals
if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
run: |
echo "No review approvals found. At least 2 approvals are required to run this action automatically."
exit 1

- name: Check for enough approvals (>=2)
id: test_variables
if: github.event_name != 'workflow_dispatch'
run: |
JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required

- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
# TODO nf-core: You can customise AWS full pipeline tests as required
Expand Down
18 changes: 10 additions & 8 deletions .github/workflows/branch.yml
Original file line number Diff line number Diff line change
@@ -1,15 +1,17 @@
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`
# This workflow is triggered on PRs to `main`/`master` branch on the repository
# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev`
on:
pull_request_target:
branches: [master]
branches:
- main
- 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
# PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
- name: Check PRs
if: github.repository == 'nf-core/callingcards'
run: |
Expand All @@ -22,7 +24,7 @@ jobs:
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
with:
message: |
## This PR is against the `master` branch :x:
## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:

* Do not close this PR
* Click _Edit_ and change the `base` to `dev`
Expand All @@ -32,9 +34,9 @@ jobs:

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.
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 }}) ${{github.event.pull_request.base.ref}} branch.
The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{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.
Expand Down
59 changes: 49 additions & 10 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -7,40 +7,79 @@ on:
pull_request:
release:
types: [published]
workflow_dispatch:

env:
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

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

jobs:
test:
name: Run pipeline with test data
name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/callingcards') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "24.04.2"
- "latest-everything"
profile:
- "conda"
- "docker"
- "singularity"
test_name:
- "test"
isMaster:
- ${{ github.base_ref == 'master' }}
# Exclude conda and singularity on dev
exclude:
- isMaster: false
profile: "conda"
- isMaster: false
profile: "singularity"
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

- name: Install Nextflow
- name: Set up Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

- name: Disk space cleanup
- name: Set up Apptainer
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-apptainer@main

- name: Set up Singularity
if: matrix.profile == 'singularity'
run: |
mkdir -p $NXF_SINGULARITY_CACHEDIR
mkdir -p $NXF_SINGULARITY_LIBRARYDIR

- name: Set up Miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
with:
miniconda-version: "latest"
auto-update-conda: true
conda-solver: libmamba
channels: conda-forge,bioconda

- name: Set up Conda
if: matrix.profile == 'conda'
run: |
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH

- name: Clean up Disk space
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- 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
- name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
Loading