From 227ded4232a57597795016ff5d521d31dc077a3f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 18 Nov 2024 11:15:49 +0100
Subject: [PATCH] update test yaml

---
 .github/workflows/test.yml | 116 +------------------------------------
 1 file changed, 2 insertions(+), 114 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index a407c387b74d..6207784dc97e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -697,6 +697,8 @@ jobs:
             profile: [docker_self_hosted, singularity]
           - path: modules/nf-core/parabricks/fq2bammeth
             profile: [docker_self_hosted, singularity]
+          - path: modules/nf-core/parabricks/dbsnp
+            profile: [docker_self_hosted, singularity]
     env:
       NXF_ANSI_LOG: false
 
@@ -714,120 +716,6 @@ jobs:
           path: ${{ matrix.path }}
           profile: ${{ matrix.profile }},gpu
 
-  nf-test-gpu:
-    runs-on: ${{ github.event.inputs.runners  || 'gpu' }}
-    name: nf-test with GPUs
-    needs: [nf-test-changes]
-    if: ( needs.nf-test-changes.outputs.paths != '[]' )
-    strategy:
-      fail-fast: false
-      matrix:
-        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
-        profile: [conda, docker_self_hosted, singularity]
-        include:
-          - path: modules/nf-core/parabricks/dbsnp
-        exclude:
-          - profile: conda
-            path: modules/nf-core/parabricks/dbsnp
-
-    env:
-      NXF_ANSI_LOG: false
-      NFTEST_VER: "0.9.0"
-      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
-      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
-
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFTEST_VER }}
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
-        id: cache-pip-pdiff
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-pdiff
-          restore-keys: |
-            ${{ runner.os }}-pip-pdiff
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pdiff cryptography
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          channels: conda-forge,bioconda
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-      # 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 nf-test
-        if: ${{ matrix.path != '' }}
-        env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
-          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
-          SENTIEON_AUTH_MECH: "GitHub Actions - token"
-        run: |
-          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
-          if [ "${{ matrix.profile }}" == "docker" ]; then
-            PROFILE="docker_self_hosted"
-          else
-            PROFILE=${{ matrix.profile }}
-          fi
-          NFT_WORKDIR=~ \
-          nf-test test \
-            --profile=${{ matrix.profile }},gpu \
-            --tap=test.tap \
-            --verbose \
-            ${{ matrix.path }}
-      - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-        if: ${{ matrix.path != '' }}
-        with:
-          path: >-
-            test.tap
-      - name: Clean up
-        if: always()
-        run: |
-          sudo rm -rf /home/ubuntu/tests/
-
   confirm-pass:
     runs-on: ubuntu-latest
     needs: