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Bump Nextflow Versions #7019

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merged 3 commits into from
Nov 19, 2024
Merged

Bump Nextflow Versions #7019

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0f464d1
ci(renovate): Add custom VERSION updates in GitHub actions
edmundmiller Nov 18, 2024
af43264
ci(#6664): Bump all Nextflow versions to 24.10.1
edmundmiller Nov 18, 2024
c1a8c7e
ci: Add renovate comments to version in actions
edmundmiller Nov 18, 2024
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4 changes: 3 additions & 1 deletion .github/actions/nf-test-action/action.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@ runs:

- name: Setup Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ env.NXF_VERSION }}"

- name: Set up Python
uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
Expand All @@ -33,7 +35,7 @@ runs:
- name: Install nf-test
uses: nf-core/setup-nf-test@v1
with:
version: "0.9.2"
version: "${{ env.NFTEST_VERSION }}"
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Don't we use NFT_VERSION in other actions?

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Yeah that's what the renovate regex had by default. We could probably get away with VER

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+1 for NFT_VERSION

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I'd say we use *_VER because that's the default env name than NXF recognize, and we used NFT_VER to be coherent.
I'd rather NFT_VER, but I'm fine with whatever as long as use the same everywhere

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ah, sorry, meant NFT_VER

install-pdiff: true

- name: Setup apptainer
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20 changes: 18 additions & 2 deletions .github/renovate.json5
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Expand Up @@ -7,8 +7,24 @@
"prHeader": "## WARNING\n - [ ] I have made sure to update the singularity and conda images",
"packageRules": [
{
"matchDatasources": ["conda", "pypi", "docker"],
"matchDatasources": [
"conda",
"pypi",
"docker"
],
"automerge": false
}
]
],
"customManagers": [
{
"customType": "regex",
"fileMatch": [
"(^|/)(workflow-templates|\\.(?:github|gitea|forgejo)/(?:workflows|actions))/.+\\.ya?ml$",
"(^|/)action\\.ya?ml$"
],
"matchStrings": [
"# renovate: datasource=(?<datasource>[a-z-.]+?) depName=(?<depName>[^\\s]+?)(?: (?:lookupName|packageName)=(?<packageName>[^\\s]+?))?(?: versioning=(?<versioning>[^\\s]+?))?(?: extractVersion=(?<extractVersion>[^\\s]+?))?\\s+[A-Za-z0-9_]+?_VERSION\\s*:\\s*[\"']?(?<currentValue>.+?)[\"']?\\s"
]
}
]
}
6 changes: 4 additions & 2 deletions .github/workflows/gpu-tests.yml
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Expand Up @@ -29,11 +29,13 @@ concurrency:

env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
NFT_VER: "0.9.2"
# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
NFTEST_VERSION: "0.9.2"
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
NXF_VER: "24.04.4"
# renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
NXF_VERSION: "24.10.1"

jobs:
nf-test-gpu:
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2 changes: 2 additions & 0 deletions .github/workflows/lint.yml
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Expand Up @@ -28,6 +28,8 @@ env:
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
NXF_VER: "24.10.1"

jobs:
pre-commit:
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6 changes: 4 additions & 2 deletions .github/workflows/nf-test.yml
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Expand Up @@ -26,11 +26,13 @@ concurrency:

env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
NFT_VER: "0.9.2"
# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
NFTEST_VERSION: "0.9.2"
NXF_ANSI_LOG: false
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
NXF_VER: "24.04.4"
# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
NXF_VERSION: "24.10.1"

jobs:
nf-test:
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4 changes: 4 additions & 0 deletions .github/workflows/pytest-workflow.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,8 @@ env:
NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
NXF_VERSION: "24.10.1"

jobs:
pytest-changes:
Expand Down Expand Up @@ -263,6 +265,8 @@ jobs:

- name: Setup Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: ${{ env.NXF_VERSION }}

- name: Setup apptainer
if: matrix.profile == 'singularity'
Expand Down
18 changes: 11 additions & 7 deletions .github/workflows/wave.yml
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Expand Up @@ -10,8 +10,12 @@ on:
# TODO Skip testing CI if any changes to environment.yml

env:
WAVE_VER: "1.5.0"
NFTEST_VER: "0.9.1"
# renovate: datasource=github-releases depName=seqeralabs/wave-cli versioning=semver
WAVE_VERSION: "1.5.0"
# renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
NFTEST_VERSION: "0.9.1"
# renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
NXF_VERSION: "24.10.1"

jobs:
generate-matrix:
Expand Down Expand Up @@ -62,8 +66,8 @@ jobs:

- name: Install wave-cli
run: |
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
chmod +x /usr/local/bin/wave

- name: Build ${{ matrix.profile }} container
Expand Down Expand Up @@ -98,8 +102,8 @@ jobs:

- name: Install wave-cli
run: |
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VERSION}/wave-${WAVE_VERSION}-linux-x86_64
sudo mv wave-${WAVE_VERSION}-linux-x86_64 /usr/local/bin/wave
chmod +x /usr/local/bin/wave

- name: Create a registry name
Expand Down Expand Up @@ -139,7 +143,7 @@ jobs:

# - uses: nf-core/setup-nf-test@v1
# with:
# version: ${{ env.NFTEST_VER }}
# version: ${{ env.NFTEST_VERSION }}

# - name: Bump Snapshot Versions
# env:
Expand Down
2 changes: 1 addition & 1 deletion tests/config/nextflow.config
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Expand Up @@ -43,5 +43,5 @@ conda { createTimeout = "120 min" }
includeConfig 'test_data.config'

manifest {
nextflowVersion = '!>=23.04.0'
nextflowVersion = '!>=24.10.1'
}
2 changes: 1 addition & 1 deletion tests/config/nf-test.config
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Expand Up @@ -56,5 +56,5 @@ conda { createTimeout = "120 min" }
includeConfig 'test_data.config'

manifest {
nextflowVersion = '!>=23.04.0'
nextflowVersion = '!>=24.10.1'
}
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