github tests + changelog

.github/workflows/main.yaml

@@ -0,0 +1,58 @@
+
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches_ignore: []
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout with submodules
+      uses: actions/checkout@v3
+      with:
+        submodules: recursive
+        fetch-depth: 0
+    - name: Formatting
+      uses: github/super-linter@v5
+      env:
+        VALIDATE_ALL_CODEBASE: false
+        DEFAULT_BRANCH: main
+        VALIDATE_SNAKEMAKE_SNAKEFMT: true
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Linting
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--lint"
+
+  run-workflow:
+    runs-on: ubuntu-latest
+    needs:
+      - linting
+      - formatting
+    steps:
+    - name: Checkout repository with submodules
+      uses: actions/checkout@v3
+      with:
+        submodules: recursive
+    - name: Test workflow
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--use-conda --use-singularity --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
+    # - name: Test report
+    #   uses: snakemake/[email protected]
+    #   with:
+    #     directory: .test
+    #     snakefile: workflow/Snakefile
+    #     args: "--use-conda --use-singularity --cores 2 --report report.zip"

CHANGELOG.md

@@ -0,0 +1,9 @@
+# 1.0.0
+
+## Features:
+
+* Snakemake v8+ compatible
+* Snakemake-wrappers
+* Relies on fair_genome_indexer version 3.0.0
+* Relies on fair_bowtie2_mapping version 3.0.1
+* Deployable workflow with integration tests on Github

README.md

@@ -3,7 +3,7 @@
 
 Do not use. Active dev.
 
-Snakemake workflow used to call peaks with Macs2 and annotate them with Homer.
+Snakemake workflow used to call variants with GATK-Mutect2
 
 ## Usage