Cleaning GH actions

.github/workflows/advanced.yaml

@@ -0,0 +1,185 @@
+name: MosaiCatcher advanced modules checks
+
+on:
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: "Log level"
+        required: true
+        default: "warning"
+        type: choice
+        options:
+          - info
+          - warning
+          - debug
+  schedule:
+    - cron: "0 0 * * 0"
+
+jobs:
+  Testing-with-MultiQC:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config MultiQC=True ashleys_pipeline=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
+
+  Testing-with-ms-norm:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config multistep_normalisation=True ashleys_pipeline=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
+
+  Testing-with-breakpointR-only:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config breakpointR=True breakpointR_only=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile
+
+  Testing-with-whatshap-only:
+    runs-on: ubuntu-latest
+    needs:
+      - Formatting
+      - Linting
+      - Testing-basic-v7
+      - Testing-basic-with-ashleys
+    steps:
+      - name: Checkout repository with submodules
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          # lfs: true
+
+      - name: Git Submodule Update
+        run: |
+          git pull --recurse-submodules
+          git submodule update --remote --recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Add Conda to system path
+        run: echo "$CONDA/bin" >> $GITHUB_PATH
+
+      - name: Install dependencies
+        run: conda install -c conda-forge mamba
+
+      - name: Setup Snakemake
+        run: mamba install -c conda-forge -c bioconda snakemake==7.32.4
+
+      - name: List options of workflow
+        run: |
+          snakemake --cores 1 --config list_commands=True --verbose --debug
+
+      - name: Run workflow
+        run: |
+          snakemake --cores 1 --use-conda --configfile .tests/config/simple_config_mosaicatcher.yaml --config whatshap_only=True \
+          --conda-frontend mamba -p --verbose --debug --snakefile workflow/Snakefile

.github/workflows/assemblies.yaml

@@ -1,9 +1,17 @@
 name: MosaiCatcher assemblies checks
 
 on:
-  push:
-    branches:
-      - "**"
+  workflow_dispatch:
+    inputs:
+      logLevel:
+        description: "Log level"
+        required: true
+        default: "warning"
+        type: choice
+        options:
+          - info
+          - warning
+          - debug
   schedule:
     - cron: "0 0 * * 0"