Merge pull request #52 from nf-core/dev

dev -> master for 0.1.0 release

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+{
+ "name": "nfcore",
+ "image": "nfcore/gitpod:latest",
+ "remoteUser": "gitpod",
+
+ // 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"]
+ }
+ }
+}

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.gitattributes

@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### 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/nf-core/viralintegration/codespaces)
+- Tools installed
+ - nf-core
+ - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
  attributes:
  label: System information
  description: |
- * Nextflow version _(eg. 21.10.3)_
+ * Nextflow version _(eg. 22.10.1)_
  * Hardware _(eg. HPC, Desktop, Cloud)_
  * Executor _(eg. slurm, local, awsbatch)_
  * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,8 +15,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/vira
 
 - [ ] 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/nf-core/viralintegration/tree/master/.github/CONTRIBUTING.md)
- - [ ] If necessary, also make a PR on the nf-core/viralintegration _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/viralintegration/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/viralintegration _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>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/awsfulltest.yml

@@ -28,6 +28,7 @@ jobs:
  "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralintegration/results-${{ github.sha }}"
  }
  profiles: test_full,aws_tower
- nextflow_config: |
- process.errorStrategy = 'retry'
- process.maxRetries = 3
+ - uses: actions/upload-artifact@v3
+ with:
+ name: Tower debug log file
+ path: tower_action_*.log

.github/workflows/awstest.yml

@@ -23,6 +23,7 @@ jobs:
  "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/viralintegration/results-test-${{ github.sha }}"
  }
  profiles: test,aws_tower
- nextflow_config: |
- process.errorStrategy = 'retry'
- process.maxRetries = 3
+ - uses: actions/upload-artifact@v3
+ with:
+ name: Tower debug log file
+ path: tower_action_*.log

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
  - name: Check PRs
  if: github.repository == 'nf-core/viralintegration'
  run: |
- "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/viralintegration ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]"
+ { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/viralintegration ]] && [[ $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
@@ -42,4 +42,3 @@ jobs:
  Thanks again for your contribution!
  repo-token: ${{ secrets.GITHUB_TOKEN }}
  allow-repeats: false
-#

.github/workflows/ci.yml

@@ -10,43 +10,74 @@ on:
 
 env:
  NXF_ANSI_LOG: false
- CAPSULE_LOG: none
+
+concurrency:
+ group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+ cancel-in-progress: true
 
 jobs:
  test:
- name: Run pipeline with test data
+ name: nf-test ${{ matrix.profile }}-${{ matrix.NXF_VER }}
  # Only run on push if this is the nf-core dev branch (merged PRs)
  if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralintegration') }}"
  runs-on: ubuntu-latest
  strategy:
  matrix:
- # Nextflow versions
- include:
- # Test pipeline minimum Nextflow version
- - NXF_VER: "21.10.3"
- NXF_EDGE: ""
- # Test latest edge release of Nextflow
- - NXF_VER: ""
- NXF_EDGE: "1"
+ NXF_VER:
+ - "22.10.1"
+ - "latest-everything"
+ profile: ["docker"] # TODO , "singularity", "conda"]
  steps:
  - name: Check out pipeline code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
+
+ - name: Cache Nextflow installation
+ id: cache-software
+ uses: actions/cache@v3
+ with:
+ path: |
+ /usr/local/bin/nextflow
+ /usr/local/bin/nf-test
+ /home/runner/.nf-test/nf-test.jar
+ key: viralintegration-${{ runner.os }}-${{ matrix.NXF_VER }}
 
  - name: Install Nextflow
- env:
- NXF_VER: ${{ matrix.NXF_VER }}
- # Uncomment only if the edge release is more recent than the latest stable release
- # See https://github.com/nextflow-io/nextflow/issues/2467
- # NXF_EDGE: ${{ matrix.NXF_EDGE }}
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: "${{ matrix.NXF_VER }}"
+
+ - name: Install nf-test
+ if: steps.cache-software.outputs.cache-hit != 'true'
  run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ wget -qO- https://code.askimed.com/install/nf-test | bash
+ sudo mv nf-test /usr/local/bin/
+
+ - name: Set up Singularity
+ if: matrix.profile == 'singularity'
+ uses: eWaterCycle/setup-singularity@v5
+ with:
+ singularity-version: 3.7.1
+
+ - name: Set up miniconda
+ if: matrix.profile == 'conda'
+ uses: conda-incubator/setup-miniconda@v2
+ with:
+ auto-update-conda: true
+ channels: conda-forge,bioconda,defaults
+ python-version: ${{ matrix.python-version }}
+
+ - name: Conda clean
+ if: matrix.profile == 'conda'
+ run: conda clean -a
 
- - 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 nf-test
  run: |
- nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+ nf-test test \
+ --profile=${{ matrix.profile }} \
+ tests/**/**/*.nf.test \
+ --tap=test.tap
 
-#
+ - uses: pcolby/tap-summary@v1
+ with:
+ path: >-
+ test.tap

.github/workflows/fix-linting.yml

@@ -0,0 +1,54 @@
+name: Fix linting from a comment
+on:
+ issue_comment:
+ types: [created]
+
+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 == 'nf-core/viralintegration'
+ 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 }}
+
+ # 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 }}
+
+ - uses: actions/setup-node@v3
+ - name: Install Prettier
+ run: npm install -g prettier @prettier/plugin-php
+
+ # Check that we actually need to fix something
+ - name: Run 'prettier --check'
+ id: prettier_status
+ run: |
+ if prettier --check ${GITHUB_WORKSPACE}; then
+ echo "result=pass" >> $GITHUB_OUTPUT
+ else
+ echo "result=fail" >> $GITHUB_OUTPUT
+ fi
+
+ - name: Run 'prettier --write'
+ if: steps.prettier_status.outputs.result == 'fail'
+ run: prettier --write ${GITHUB_WORKSPACE}
+
+ - 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

.github/workflows/linting.yml

@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
  push:
+ branches:
+ - dev
  pull_request:
  release:
  types: [published]
@@ -12,9 +14,9 @@ jobs:
  EditorConfig:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: actions/setup-node@v2
+ - uses: actions/setup-node@v3
 
  - name: Install editorconfig-checker
  run: npm install -g editorconfig-checker
@@ -25,32 +27,58 @@ jobs:
  Prettier:
  runs-on: ubuntu-latest
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: actions/setup-node@v2
+ - uses: actions/setup-node@v3
 
  - name: Install Prettier
  run: npm install -g prettier
 
  - name: Run Prettier --check
  run: prettier --check ${GITHUB_WORKSPACE}
 
+ PythonBlack:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v3
+
+ - name: Check code lints with Black
+ uses: psf/black@stable
+
+ # If the above check failed, post a comment on the PR explaining the failure
+ - name: Post PR comment
+ if: failure()
+ uses: mshick/add-pr-comment@v1
+ with:
+ message: |
+ ## Python linting (`black`) is failing
+
+ To keep the code consistent with lots of contributors, we run automated code consistency checks.
+ To fix this CI test, please run:
+
+ * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
+ * Fix formatting errors in your pipeline: `black .`
+
+ Once you push these changes the test should pass, and you can hide this comment :+1:
+
+ We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
+
+ Thanks again for your contribution!
+ repo-token: ${{ secrets.GITHUB_TOKEN }}
+ allow-repeats: false
+
  nf-core:
  runs-on: ubuntu-latest
  steps:
  - name: Check out pipeline code
- uses: actions/checkout@v2
+ uses: actions/checkout@v3
 
  - name: Install Nextflow
- env:
- CAPSULE_LOG: none
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ uses: nf-core/setup-nextflow@v1
 
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
  with:
- python-version: "3.6"
+ python-version: "3.7"
  architecture: "x64"
 
  - name: Install dependencies
@@ -71,12 +99,10 @@ jobs:
 
  - name: Upload linting log file artifact
  if: ${{ always() }}
- uses: actions/upload-artifact@v2
+ uses: actions/upload-artifact@v3
  with:
  name: linting-logs
  path: |
  lint_log.txt
  lint_results.md
  PR_number.txt
-
-#

.github/workflows/linting_comment.yml

@@ -18,12 +18,11 @@ jobs:
 
  - name: Get PR number
  id: pr_number
- run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+ run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
  - name: Post PR comment
  uses: marocchino/sticky-pull-request-comment@v2
  with:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  number: ${{ steps.pr_number.outputs.pr_number }}
  path: linting-logs/lint_results.md
-#

.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+.nf-test