From 3557ae9514d65a711e5c4d5ac1da861dbac4fb96 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Thu, 20 Jul 2023 10:21:19 +0100
Subject: [PATCH] run pytest workflow

---
 .github/workflows/ci.yml     | 37 ++++++++++++++++++
 .github/workflows/module.yml | 73 ++++++++++++++++++++++++++++++++++++
 2 files changed, 110 insertions(+)
 create mode 100644 .github/workflows/module.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 40d09781..6ff2b930 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -33,3 +33,40 @@ jobs:
       cache-key: ${{ needs.preload_singularity.outputs.cache-key }}
       singularity: true
 
+  pytest_workflow_docker:
+    needs: preload_docker
+    uses: ./.github/workflows/module.yml
+    strategy:
+      matrix:
+        tags:
+          - "test input check subworkflow"
+          - "test input check subworkflow with PGS catalog API"
+          - "test input check subworkflow with PGS catalog API and whitespace"
+          - "test make compatible subworkflow with bfile"
+          - "test make compatible subworkflow with vcf"
+          - "test make compatible subworkflow with pfile"
+          - "test input check subworkflow with liftover 38to37"
+          - "test input check subworkflow with liftover 37to38"
+          - "test apply score subworkflow"
+          - "test perfect apply score"
+          - "test combine scorefiles module"
+          - "test match module"
+          - "test match combine module"
+          - "plink2 testrelabelpvar"
+          - "plink2 testscore"
+          - "plink2 testsmallscore"
+          - "plink2 testmultiscore"
+          - "plink2 testsmallmultiscore"
+          - "plink2 testmultiscorefail"
+          - "plink2 vcf"
+          - "plink2 testrelabelbim"
+          - "pgscatalog test --pgs_id"
+          - "pgscatalog test --efo_trait --pgp_id and --pgs_id"
+          - "pgscatalog test bad accession"
+          - "pgscatalog test good and bad accessions GRCh38"
+    with:
+      cache-key: ${{ needs.preload_docker.outputs.cache-key }}
+      docker: true
+      tag: ${{ matrix.tags }}
+      
+  
diff --git a/.github/workflows/module.yml b/.github/workflows/module.yml
new file mode 100644
index 00000000..cb10ae2d
--- /dev/null
+++ b/.github/workflows/module.yml
@@ -0,0 +1,73 @@
+name: Run pytest-workflow
+
+on:
+  workflow_call:
+    inputs:
+      cache-key:
+        type: string
+        required: true
+      docker:
+        type: boolean
+      singularity:
+        type: boolean
+      tag:
+        type: string
+        required: true
+
+env:
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/singularity
+  SINGULARITY_VERSION: 3.8.3
+  
+jobs:
+  docker:
+    if: ${{ inputs.docker }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - uses: nf-core/setup-nextflow@v1
+        with:
+          version: ${{ matrix.nxf_ver }}
+
+      - name: Restore docker images
+        if: matrix.profile == 'docker'
+        id: restore-docker
+        uses: actions/cache/restore@v3
+        with:
+          path: ${{ runner.temp }}/docker
+          key: ${{ inputs.cache-key }}
+
+      - name: Load docker images from cache
+        if: steps.restore-docker.outputs.cache-hit == 'true'
+        run: |
+          find $HOME -name '*.tar'
+          find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \;
+
+      - name: Set up test requirements
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - run: pip install -r ${{ github.workspace }}/tests/requirements.txt          
+
+      - name: Run unit tests
+        run: TMPDIR=~ PROFILE=docker pytest --kwdof --symlink --git-aware --wt 2 --tag "${{ inputs.tag }}" --ignore tests/bin
+
+      - name: Upload logs on failure
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: logs-docker-${{ inputs.tag }}
+          path: |
+            /home/runner/pytest_workflow_*/*/.nextflow.log
+            /home/runner/pytest_workflow_*/*/log.out
+            /home/runner/pytest_workflow_*/*/log.err
+            /home/runner/pytest_workflow_*/*/work
+            !/home/runner/pytest_workflow_*/*/work/conda
+            !/home/runner/pytest_workflow_*/*/work/singularity
+
+