add new workflow

.github/workflows/sing.yml

@@ -0,0 +1,58 @@
+name: Tests
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches-ignore: []
+  schedule:
+    - cron: '0 0 * * SUN'
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        python: [3.7, 3.8, 3.9]
+      fail-fast: false
+
+
+    steps:
+
+    - name: install graphviz
+      run: |
+        sudo apt-get install -y graphviz
+
+    - name: checkout git repo
+      uses: actions/checkout@v2
+
+    - name: Set up Python 3.X
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+
+    - name: conda
+      run: |
+        conda install -c conda-forge  -c bioconda --quiet -y python=${{ matrix.python }} singularity
+
+    - name: Install dependencies
+      run: |
+        pip install .[testing]
+
+    - name: install package itself
+      run: |
+         pip install .
+
+    - name: testing
+      run: |
+        sequana_variant_calling --input-directory test/data/ --use-singularity  --reference-file test/data/JB409847.fasta && cd variant_calling && sh variant_calling
+
+

README.rst

@@ -127,6 +127,7 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+0.11.1    * Updae rule sambamba to use latest wrappers
 0.11.0    * Add singularity containers
 0.10.0    * fully integrated sequana wrappers and simplification of HTML reports
 0.9.10    * Uses new sequana_pipetools and wrappers

setup.py

@@ -6,7 +6,7 @@
 
 _MAJOR               = 0
 _MINOR               = 11
-_MICRO               = 0
+_MICRO               = 1
 
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)