From 76884d2a3d9dc9dfbc31b788026e0ac6ee7decaf Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Wed, 17 Jul 2024 09:29:42 -0500
Subject: [PATCH] ci: Add Sentieon logic to pytest-workflow

---
 .github/workflows/test.yml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index eb7144b5fd0..45c55a3bb07 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -408,6 +408,8 @@ jobs:
             tags: vt/decompose
     env:
       NXF_ANSI_LOG: false
+      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
+      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
 
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
@@ -462,8 +464,20 @@ jobs:
           echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
           echo $(realpath python) >> $GITHUB_PATH
 
+      # FIXME Remove once https://github.com/nf-core/sarek/issues/1380 is closed
+      # Set up secrets
+      - name: Set up nextflow secrets
+        # 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 "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")
+
       # Test the module
       - name: Run pytest-workflow
+        # FIXME Remove once https://github.com/nf-core/sarek/issues/1380 is closed
+        env:
+          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
+          SENTIEON_AUTH_MECH: "GitHub Actions - token"
         # only use one thread for pytest-workflow to avoid race condition on conda cache.
         run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes