From c5e47946784044dfd87ac8168c78941964f61b9a Mon Sep 17 00:00:00 2001
From: tdayris <thibault.dayris@gustaveroussy.fr>
Date: Fri, 26 Jan 2024 12:19:06 +0100
Subject: [PATCH] github tests + changelog

---
 .github/workflows/main.yaml | 58 +++++++++++++++++++++++++++++++++++++
 CHANGELOG.md                |  9 ++++++
 README.md                   |  2 +-
 3 files changed, 68 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/main.yaml
 create mode 100644 CHANGELOG.md

diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
new file mode 100644
index 0000000..b9d213b
--- /dev/null
+++ b/.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/snakemake-github-action@v1.25.1
+      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/snakemake-github-action@v1.25.1
+      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/snakemake-github-action@v1.25.1
+    #   with:
+    #     directory: .test
+    #     snakefile: workflow/Snakefile
+    #     args: "--use-conda --use-singularity --cores 2 --report report.zip"
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..09addc5
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/README.md b/README.md
index 9da4be9..b8d8821 100644
--- a/README.md
+++ b/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