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Fix Sentieon CI #5934

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merged 3 commits into from
Jul 8, 2024
Merged

Fix Sentieon CI #5934

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8d32584
ci: Remove setting secrets in pytest-workflow
edmundmiller Jul 8, 2024
1c90924
ci: Add a longer note about conditionals
edmundmiller Jul 8, 2024
903ec1d
ci: Check for secrets in env
edmundmiller Jul 8, 2024
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22 changes: 5 additions & 17 deletions .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -408,7 +408,6 @@ jobs:
tags: vt/decompose
env:
NXF_ANSI_LOG: false
SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}

steps:
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
Expand Down Expand Up @@ -463,17 +462,6 @@ jobs:
echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
echo $(realpath python) >> $GITHUB_PATH

# Set up secrets
- name: Set up nextflow secrets
if: env.SENTIEON_LICENSE_BASE64 != null
env:
SENTIEON_LICENSE: ${{ secrets.LICSRVR_IP }}
SENTIEON_AUTH_MECH: "GitHub Actions - token"
ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
run: |
nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "$SENTIEON_LICENSE_MESSAGE")

# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
Expand Down Expand Up @@ -649,6 +637,8 @@ jobs:
env:
NXF_ANSI_LOG: false
NFTEST_VER: "0.8.4"
SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}

steps:
- uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
Expand Down Expand Up @@ -705,12 +695,10 @@ jobs:

# Set up secrets
- name: Set up nextflow secrets
# FIXME if: secrets.SENTIEON_ENCRYPTION_KEY != null
env:
SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
# TODO Only run if the tag includes `sentieon`
if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null
run: |
nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "$SENTIEON_LICENSE_MESSAGE")
nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")

# Test the module
- name: Run nf-test
Expand Down
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