Merge pull request #1650 from MillironX/feature/setup-nextflow-action

Switch CI to nf-core/setup-nextflow action

.github/workflows/create-lint-wf.yml

@@ -3,7 +3,6 @@ on: [push, pull_request]
 
 env:
  NXF_ANSI_LOG: false
- CAPSULE_LOG: none
 
 jobs:
  MakeTestWorkflow:
@@ -12,14 +11,9 @@ jobs:
  NXF_ANSI_LOG: false
  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:
+ - "21.10.3"
+ - "latest-everything"
  steps:
  # Get the repo code
  - uses: actions/checkout@v2
@@ -38,14 +32,9 @@ jobs:
 
  # Set up Nextflow
  - 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 }}
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: ${{ matrix.NXF_VER }}
 
  # Install the Prettier linting tools
  - uses: actions/setup-node@v2

.github/workflows/create-test-wf.yml

@@ -3,7 +3,6 @@ on: [push, pull_request]
 
 env:
  NXF_ANSI_LOG: false
- CAPSULE_LOG: none
 
 jobs:
  RunTestWorkflow:
@@ -12,14 +11,9 @@ jobs:
  NXF_ANSI_LOG: false
  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:
+ - "21.10.3"
+ - "latest-everything"
  steps:
  - uses: actions/checkout@v2
  name: Check out source-code repository
@@ -35,14 +29,9 @@ jobs:
  pip install .
 
  - 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 }}
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: ${{ matrix.NXF_VER }}
 
  - name: Run nf-core/tools
  run: |

.github/workflows/pytest.yml

@@ -5,9 +5,6 @@ on:
  push:
  pull_request:
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
  pytest:
  runs-on: ubuntu-latest
@@ -30,11 +27,9 @@ jobs:
  pip install -e .
 
  - 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
+ with:
+ version: "latest-everything"
 
  - name: Test with pytest
  run: python3 -m pytest tests/ --color=yes --cov-report=xml --cov-config=.github/.coveragerc --cov=nf_core

.github/workflows/sync.yml

@@ -9,9 +9,6 @@ on:
  description: Only run on nf-core/testpipeline?
  required: true
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
  get-pipelines:
  runs-on: ubuntu-latest
@@ -57,13 +54,9 @@ jobs:
  pip install .
 
  - name: Install Nextflow
- env:
- CAPSULE_LOG: none
- run: |
- mkdir /tmp/nextflow
- cd /tmp/nextflow
- wget -qO- get.nextflow.io | bash
- sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: "latest-everything"
 
  - name: Run synchronisation
  if: github.repository == 'nf-core/tools'

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Template
 
 - Fix bug in pipeline readme logo URL ([#1590](https://github.com/nf-core/tools/pull/1590))
+- Switch CI to use [setup-nextflow](https://github.com/nf-core/setup-nextflow) action to install Nextflow ([#1650](https://github.com/nf-core/tools/pull/1650))
 
 ### Linting
 
@@ -19,6 +20,7 @@
 - Updated the package requirements to prevent defunct installations of nf-core ([#1620](https://github.com/nf-core/tools/pull/1620))
 - Fix and improve broken test for Singularity container download ([#1622](https://github.com/nf-core/tools/pull/1622))
 - Use [`$XDG_CACHE_HOME`](https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html) or `~/.cache` instead of `$XDG_CONFIG_HOME` or `~/config/` as base directory for API cache
+- Switch CI to use [setup-nextflow](https://github.com/nf-core/setup-nextflow) action to install Nextflow ([#1650](https://github.com/nf-core/tools/pull/1650))
 
 ### Modules
 

nf_core/bump_version.py

@@ -83,9 +83,11 @@ def bump_nextflow_version(pipeline_obj, new_version):
  pipeline_obj,
  [
  (
- # example: - NXF_VER: '20.04.0'
- rf"- NXF_VER: [\'\"]{re.escape(current_version)}[\'\"]",
- f"- NXF_VER: '{new_version}'",
+ # example:
+ # NXF_VER:
+ # - "20.04.0"
+ rf"- [\"]{re.escape(current_version)}[\"]",
+ f'- "{new_version}"',
  )
  ],
  )

nf_core/lint/actions_ci.py

@@ -137,8 +137,8 @@ def actions_ci(self):
 
  # Check that we are testing the minimum nextflow version
  try:
- matrix = ciwf["jobs"]["test"]["strategy"]["matrix"]["include"]
- assert any([i.get("NXF_VER") == self.minNextflowVersion for i in matrix])
+ nxf_ver = ciwf["jobs"]["test"]["strategy"]["matrix"]["NXF_VER"]
+ assert any([i == self.minNextflowVersion for i in nxf_ver])
  except (KeyError, TypeError):
  failed.append("'.github/workflows/ci.yml' does not check minimum NF version")
  except AssertionError:

nf_core/pipeline-template/.github/workflows/ci.yml

@@ -10,7 +10,6 @@ on:
 
 env:
  NXF_ANSI_LOG: false
- CAPSULE_LOG: none
 
 jobs:
  test:
@@ -20,31 +19,21 @@ jobs:
  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 {%- raw %}
- - NXF_VER: ""
- NXF_EDGE: "1"
+ NXF_VER:
+ - "21.10.3"
+ - "latest-everything"
  steps:
  - name: Check out pipeline code
  uses: actions/checkout@v2
 
  - 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: ${{ matrix.NXF_EDGE }}
- run: |
- wget -qO- get.nextflow.io | bash
- sudo mv nextflow /usr/local/bin/
+ uses: nf-core/setup-nextflow@v1
+ with:
+ version: "{% raw %}${{ matrix.NXF_VER }}{% endraw %}"
 
  - 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
  run: |
- nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results {%- endraw %}
+ nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

nf_core/pipeline-template/.github/workflows/linting.yml

@@ -42,11 +42,7 @@ jobs:
  uses: actions/checkout@v2
 
  - 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@v3
  with:

tests/test_bump_version.py

@@ -63,8 +63,9 @@ def test_bump_nextflow_version(datafiles, tmp_path):
  pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
  pipeline_obj._load()
 
- # Bump the version number to a specific version
- version = "21.10.3"
+ # Bump the version number to a specific version, preferably one
+ # we're not already on
+ version = "22.04.3"
  nf_core.bump_version.bump_nextflow_version(pipeline_obj, version)
  new_pipeline_obj = nf_core.utils.Pipeline(test_pipeline_dir)
 
@@ -75,7 +76,7 @@ def test_bump_nextflow_version(datafiles, tmp_path):
  # Check .github/workflows/ci.yml
  with open(new_pipeline_obj._fp(".github/workflows/ci.yml")) as fh:
  ci_yaml = yaml.safe_load(fh)
- assert ci_yaml["jobs"]["test"]["strategy"]["matrix"]["include"][0]["NXF_VER"] == version
+ assert ci_yaml["jobs"]["test"]["strategy"]["matrix"]["NXF_VER"][0] == version
 
  # Check README.md
  with open(new_pipeline_obj._fp("README.md")) as fh: