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Add GPU-based tests #6953
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Add GPU-based tests #6953
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d946f4d
split nf-test section into its own action.yml and add gpu test cases
mashehu 473857e
add gpu profile
mashehu 09bc2d3
Update test.yml
mashehu 3514f77
add checkout action before running nf-test action
mashehu 88fbfe3
Merge branch 'add-gpu-tests' of github.com:mashehu/modules into add-g…
mashehu 51f66e1
add miniconda-setup step
mashehu 616e0ef
Update tests/config/nextflow.config
mashehu 7cb14f4
try to fix composite action
mashehu 3a164c9
Merge branch 'add-gpu-tests' of github.com:mashehu/modules into add-g…
mashehu 36897d8
Merge branch 'master' into add-gpu-tests
mashehu 0bdcbb2
add profile info to include step, to avoid empty profile values
mashehu 18de958
Merge branch 'add-gpu-tests' of github.com:mashehu/modules into add-g…
mashehu e9d237b
touch fastqc to kick of some tests
mashehu 004b9a6
add gpu profile to nf-test.config
mashehu 834614a
Merge branch 'master' of github.com:nf-core/modules into add-gpu-tests
mashehu 660d68f
fix miniconda setup step
mashehu f90f4c2
remove miniconda version pin
mashehu 12115c4
try to exclude all non-gpu tests
mashehu 236276d
remove changed paths
mashehu 88494a6
add check for changes in parabricks
mashehu d50b3cb
fix pip error
mashehu 6fa8d59
add setup-python to main script
mashehu b2de5f7
remove conda defaults channels
mashehu 4609f2c
Merge branch 'master' into add-gpu-tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| name: "nf-test Action" | ||
| description: "Runs nf-test with common setup steps" | ||
| inputs: | ||
| path: | ||
| description: "Path to test" | ||
| required: true | ||
| profile: | ||
| description: "Profile to use" | ||
| required: true | ||
|
|
||
| runs: | ||
| using: "composite" | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - uses: actions/setup-java@v4 | ||
| with: | ||
| distribution: "temurin" | ||
| java-version: "17" | ||
|
|
||
| - name: Setup Nextflow | ||
| uses: nf-core/setup-nextflow@v2 | ||
|
|
||
| - name: Set up Python | ||
| uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 | ||
| with: | ||
| python-version: "3.11" | ||
|
|
||
| - name: Install nf-test | ||
| uses: nf-core/setup-nf-test@v1 | ||
| with: | ||
| version: "0.9.2" | ||
| install-pdiff: true | ||
|
|
||
| - name: Setup apptainer | ||
| if: contains(inputs.profile, 'singularity') | ||
| uses: eWaterCycle/setup-apptainer@main | ||
|
|
||
| - name: Set up Singularity | ||
| if: contains(inputs.profile, 'singularity') | ||
| shell: bash | ||
| run: | | ||
| mkdir -p $NXF_SINGULARITY_CACHEDIR | ||
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | ||
|
|
||
| - name: Conda setup | ||
| if: ${{inputs.profile == 'conda'}} | ||
| uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 | ||
| with: | ||
| auto-update-conda: true | ||
| conda-solver: libmamba | ||
| conda-remove-defaults: true | ||
|
|
||
| # Set up secrets | ||
| - name: Set up nextflow secrets | ||
| if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != '' | ||
| shell: bash | ||
| run: | | ||
| nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE") | ||
|
|
||
| - name: Run nf-test | ||
| shell: bash | ||
| env: | ||
| SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }} | ||
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | ||
| run: | | ||
| NFT_WORKDIR=~ \ | ||
| nf-test test \ | ||
| --profile=${{ inputs.profile }} \ | ||
| --tap=test.tap \ | ||
| --verbose \ | ||
| ${{ inputs.path }} | ||
| - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 | ||
| if: ${{ inputs.path != '' }} | ||
| with: | ||
| path: >- | ||
| test.tap | ||
|
|
||
| - name: Clean up | ||
| if: always() | ||
| shell: bash | ||
| run: | | ||
| sudo rm -rf /home/ubuntu/tests/ |
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Will this trigger tests for these three modules whenever
if: ( needs.nf-test-changes.outputs.paths != '[]' )is true.