v2 release

.github/workflows/ancestry.yml

@@ -0,0 +1,148 @@
+name: Run ancestry test with singularity or docker profiles
+
+on:
+  workflow_call:
+    inputs:
+      container-cache-key:
+        type: string
+        required: true
+      ancestry-cache-key:
+        type: string
+        required: true
+      docker:
+        type: boolean
+      singularity:
+        type: boolean
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity
+  SINGULARITY_VERSION: 3.8.3
+
+jobs:
+  docker:
+    if: ${{ inputs.docker }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set environment variables
+        run: |
+          echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+          echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - uses: nf-core/setup-nextflow@v1
+
+      - name: Restore docker images
+        id: restore-docker
+        uses: actions/cache/restore@v3
+        with:
+          path: ${{ runner.temp }}/docker
+          key: ${{ inputs.container-cache-key }}
+          fail-on-cache-miss: true
+
+      - name: Load docker images from cache
+        run: |
+          find $HOME -name '*.tar'
+          find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \;
+
+      - name: Restore reference data
+        uses: actions/cache/restore@v3
+        with:
+          path: |
+            ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
+            ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam
+            ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst
+            ${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst
+          key: ${{ inputs.ancestry-cache-key }}
+          fail-on-cache-miss: true
+
+      - name: Set up test requirements
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+
+      - run: pip install -r ${{ github.workspace }}/tests/requirements.txt
+
+      - name: Run ancestry test
+        run: TMPDIR=~ PROFILE=docker pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: logs-singularity-ancestry
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/output/*
+
+  singularity:
+    if: ${{ inputs.singularity }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Set environment variables
+        run: |
+          echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+          echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
+
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - uses: nf-core/setup-nextflow@v1
+
+      - name: Restore singularity setup
+        id: restore-singularity-setup
+        uses: actions/cache@v3
+        with:
+          path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
+          key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
+          fail-on-cache-miss: true
+
+      - name: Add singularity to path
+        run: |
+          echo "/opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64/bin" >> $GITHUB_PATH
+
+      - name: Restore singularity container images
+        id: restore-singularity
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
+          key: ${{ inputs.container-cache-key }}
+
+      - name: Restore reference data
+        uses: actions/cache/restore@v3
+        with:
+          path: |
+            ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
+            ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.psam
+            ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pvar.zst
+            ${{ env.ANCESTRY_REF_DIR }}/GRCh38_HAPNEST_reference.tar.zst
+          key: ${{ inputs.ancestry-cache-key }}
+          fail-on-cache-miss: true
+
+      - name: Set up test requirements
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+
+      - run: pip install -r ${{ github.workspace }}/tests/requirements.txt
+
+      - name: Run ancestry test
+        run: TMPDIR=~ PROFILE=singularity pytest --kwdof --symlink --git-aware --wt 2 --tag "ancestry" --ignore tests/bin
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: logs-singularity-ancestry
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/output/*