Merge pull request #46 from rki-mf1/ci

CI restructuring

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,31 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+- **Describe the bug**
+A clear and concise description of what the bug is.
+
+- **To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+- **Expected behavior**
+A clear and concise description of what you expected to happen.
+
+- **Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+- **Desktop (please complete the following information):**
+- - OS: [e.g. Linux, ...]
+- - Version [e.g. cievad v0.1.0]
+
+- **Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,17 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+- **Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+- **Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+- **Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/tests.yml

@@ -1,15 +1,15 @@
-name: CI
+name: tests
 
 on:
   push:
     branches: [ "main", "dev", "ci" ]
   pull_request:
-    branches: [ "main" ]
+    branches: [ "main", "dev" ]
 
 # designed as in: https://github.com/marketplace/actions/setup-miniconda
 jobs:
-  CI:
-    name: CI (Linux)
+  build:
+    name: build nf env
     runs-on: "ubuntu-latest"
     defaults:
       run:
@@ -36,6 +36,25 @@ jobs:
         run: |
           nextflow -version
 
+
+  run-hap:
+    name: Run hap.nf
+    needs: build
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: nextflow
+          environment-file: env/conda_nxf.yml
+          channels: conda-forge,bioconda,defaults
+          channel-priority: true
+          auto-activate-base: false
+
       - name : Download reference
         run: |
           wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
@@ -47,6 +66,31 @@ jobs:
         run: |
           nextflow run hap.nf -profile local,conda
 
+  run-eval:
+    name: Run eval.nf
+    needs: build
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: nextflow
+          environment-file: env/conda_nxf.yml
+          channels: conda-forge,bioconda,defaults
+          channel-priority: true
+          auto-activate-base: false
+
+      - name : Download reference
+        run: |
+          wget https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3
+          sed 's/>ENA|MN908947|MN908947.3 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome./>MN908947.3/g' MN908947.3 > MN908947.3.fasta
+          mkdir -p reference/Sars-Cov-2/Wuhan-Hu-1/
+          mv MN908947.3.fasta reference/Sars-Cov-2/Wuhan-Hu-1/
+
       - name: Test callset evaluation
         run: |
           nextflow run eval.nf -profile local,conda --callsets_dir aux/ci_data/