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Merge pull request #318 from nf-core/dev
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Release v2.6.0
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grst authored May 7, 2024
2 parents 90cb6a4 + 7be5e57 commit c5a6445
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16 changes: 4 additions & 12 deletions .devcontainer/devcontainer.json
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Expand Up @@ -10,19 +10,11 @@
"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.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
},
},
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}
15 changes: 14 additions & 1 deletion .editorconfig
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Expand Up @@ -18,7 +18,20 @@ end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset
[/subworkflows/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset

[/assets/email*]
indent_size = unset

# ignore Readme
[README.md]
indent_style = unset

# ignore python
[*.{py,md}]
indent_style = unset
14 changes: 8 additions & 6 deletions .github/CONTRIBUTING.md
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Expand Up @@ -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/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::
> [!NOTE]
> If you need help using or modifying nf-core/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
## Contribution workflow

Expand All @@ -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.
Expand Down Expand Up @@ -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

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2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/scrn
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/scrnaseq/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/scrnaseq _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.
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2 changes: 1 addition & 1 deletion .github/workflows/awsfulltest.yml
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Expand Up @@ -31,7 +31,7 @@ jobs:
}
profiles: test_full

- uses: actions/upload-artifact@v3
- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
path: |
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3 changes: 2 additions & 1 deletion .github/workflows/awstest.yml
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Expand Up @@ -28,7 +28,8 @@ jobs:
"aligner": "${{ matrix.aligner }}"
}
profiles: test
- uses: actions/upload-artifact@v3

- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
path: |
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2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
# 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
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
with:
message: |
## This PR is against the `master` branch :x:
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69 changes: 46 additions & 23 deletions .github/workflows/ci.yml
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@@ -1,56 +1,79 @@
name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
name: nf-core CI
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
merge_group:
types:
- checks_requested
branches:
- master
- dev

env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.8.1"

concurrency:
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
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)
name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}"
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
profile: [
"test,docker --aligner alevin",
"test,docker --aligner kallisto",
"test,docker --aligner star",
"test,docker --aligner cellranger",
# "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
# "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
]
profile: ["alevin", "cellranger", "kallisto", "star"]

steps:
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: Check out pipeline code
uses: actions/checkout@v4
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

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

- name: Run pipeline with test data
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
- name: Cache nf-test installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest

- name: Install nf-test
if: steps.cache-software.outputs.cache-hit != 'true'
run: |
wget -qO- https://code.askimed.com/install/nf-test | bash
sudo mv nf-test /usr/local/bin/
- name: Run nf-test
run: |
nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} --outdir ./results
nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml
- name: Output log on failure
if: failure()
run: |
sudo apt install bat > /dev/null
batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: test.xml
2 changes: 1 addition & 1 deletion .github/workflows/clean-up.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
issues: write
pull-requests: write
steps:
- uses: actions/stale@v7
- uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # 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."
Expand Down
75 changes: 75 additions & 0 deletions .github/workflows/download_pipeline.yml
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@@ -0,0 +1,75 @@
name: Test successful pipeline download with 'nf-core download'

# Run the workflow when:
# - dispatched manually
# - when a PR is opened or reopened to master branch
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
workflow_dispatch:
inputs:
testbranch:
description: "The specific branch you wish to utilize for the test execution of nf-core download."
required: true
default: "dev"
pull_request:
types:
- opened
branches:
- master
pull_request_target:
branches:
- master

env:
NXF_ANSI_LOG: false

jobs:
download:
runs-on: ubuntu-latest
steps:
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

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

- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.11"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
singularity-version: 3.8.3

- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install git+https://github.com/nf-core/tools.git@dev
- name: Get the repository name and current branch set as environment variable
run: |
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
run: |
nf-core download ${{ env.REPO_LOWERCASE }} \
--revision ${{ env.REPO_BRANCH }} \
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
--compress "none" \
--container-system 'singularity' \
--container-library "quay.io" -l "docker.io" -l "ghcr.io" \
--container-cache-utilisation 'amend' \
--download-configuration
- name: Inspect download
run: tree ./${{ env.REPOTITLE_LOWERCASE }}

- name: Run the downloaded pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
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