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Important! Template update for nf-core/tools v2.14.0 #267

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11 changes: 2 additions & 9 deletions .devcontainer/devcontainer.json
Original file line number Diff line number Diff line change
Expand Up @@ -2,22 +2,15 @@
"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"
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},

// Add the IDs of extensions you want installed when the container is created.
Expand Down
11 changes: 10 additions & 1 deletion .editorconfig
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,16 @@ 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 python and markdown
[*.{py,md}]
indent_style = unset
10 changes: 8 additions & 2 deletions .github/CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ 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 ;)

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

## Contribution workflow
Expand All @@ -25,6 +26,12 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

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 @@ -85,7 +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

Expand Down Expand Up @@ -116,4 +123,3 @@ To get started:
Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ body:
attributes:
label: System information
description: |
* Nextflow version _(eg. 22.10.1)_
* 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)_
Expand Down
1 change: 1 addition & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/nano
- [ ] If necessary, also make a PR on the nf-core/nanoseq _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>`).
- [ ] 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.
Expand Down
19 changes: 12 additions & 7 deletions .github/workflows/awsfulltest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -8,27 +8,32 @@ on:
types: [published]
workflow_dispatch:
jobs:
run-tower:
run-platform:
name: Run AWS full tests
if: github.repository == 'nf-core/nanoseq'
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
- name: Launch workflow via Seqera Platform
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
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nanoseq/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nanoseq/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
- uses: actions/upload-artifact@v3
profiles: test_full

- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
path: tower_action_*.log
name: Seqera Platform debug log file
path: |
seqera_platform_action_*.log
seqera_platform_action_*.json
20 changes: 12 additions & 8 deletions .github/workflows/awstest.yml
Original file line number Diff line number Diff line change
Expand Up @@ -5,25 +5,29 @@ name: nf-core AWS test
on:
workflow_dispatch:
jobs:
run-tower:
run-platform:
name: Run AWS tests
if: github.repository == 'nf-core/nanoseq'
runs-on: ubuntu-latest
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
# Launch workflow using Seqera Platform CLI tool action
- name: Launch workflow via Seqera Platform
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nanoseq/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nanoseq/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
- uses: actions/upload-artifact@v3
profiles: test

- uses: actions/upload-artifact@v4
with:
name: Tower debug log file
path: tower_action_*.log
name: Seqera Platform debug log file
path: |
seqera_platform_action_*.log
seqera_platform_action_*.json
2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
Original file line number Diff line number Diff line change
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:
Expand Down
9 changes: 6 additions & 3 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,17 +24,20 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"

- name: Disk space cleanup
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
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/clean-up.yml
Original file line number Diff line number Diff line change
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
86 changes: 86 additions & 0 deletions .github/workflows/download_pipeline.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
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
- edited
- synchronize
branches:
- master
pull_request_target:
branches:
- master

env:
NXF_ANSI_LOG: false

jobs:
download:
runs-on: ubuntu-latest
steps:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2

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

- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
with:
python-version: "3.12"
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 (stub)
id: stub_run_pipeline
continue-on-error: true
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
- name: Run the downloaded pipeline (stub run not supported)
id: run_pipeline
if: ${{ job.steps.stub_run_pipeline.status == failure() }}
env:
NXF_SINGULARITY_CACHEDIR: ./
NXF_SINGULARITY_HOME_MOUNT: true
run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
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