create sequana_pipelines

.github/workflows/main.yml

@@ -22,8 +22,10 @@ jobs:
     steps:
 
     - uses: actions/checkout@v3
+
     - name: Install poetry
       run: pipx install poetry
+
     - name: Setup python 3.X
       uses: actions/setup-python@v4
       with:

.github/workflows/pypi.yml

@@ -10,30 +10,32 @@ jobs:
     name: Build and publish to PyPI and TestPyPI
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@main
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v3
+
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.9
 
-    - name: Install package
-      run: |
-          pip install build
+    - name: Install poetry
+      run: pipx install poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
-          python setup.py sdist
+          poetry build
+
+    - name: Config Test PyPI
+      run: |
+          poetry config repositories.testpypi https://test.pypi.org/legacy/
+          poetry config pypi-token.testpypi ${{ secrets.TEST_PYPI_API_KEY }}
 
     - name: Publish distribution to Test PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-        repository_url: https://test.pypi.org/legacy/
+      run: poetry publish -r testpypi
+
+    - name: Config PyPI
+      run: poetry config pypi-token.pypi ${{ secrets.PYPI_API_KEY }}
+
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      run: poetry publish

README.md

@@ -6,7 +6,7 @@
 [![PyPI version](https://badge.fury.io/py/mergegi.svg)](https://badge.fury.io/py/mergegi)
 
 
-**MergeGI** provides a single command line to merge and select barcoded raw data from [MGI](https://en.mgi-tech.com/products/) sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis. 
+**MergeGI** provides a single command line to merge and select barcoded raw data from [MGI](https://en.mgi-tech.com/products/) sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis.
 
 
 - [Installation](#installation)
@@ -16,7 +16,7 @@
 
 ## Installation
 
-We provide **MergeGI** as a Python library available on [Pypi](https://pypi.python.org). The standalone application is called **mergegi** and can be installed in an environment with Python>3.6 as follows:
+We provide **MergeGI** as a Python library available on [Pypi](https://pypi.python.org). The standalone application is called **mergegi** and can be installed in an environment with Python>3.7 as follows:
 
     pip install mergegi
 
@@ -27,13 +27,26 @@ For developers:
 
     git clone git@github.com:sequana/MergeGI.git
     cd MergeGI
-    pip install -e .[testing]
+    poetry install
+    poetry shell
+
+We also provide a pipeline for demultiplexing MGI data in Snakemake, which can be installed as an extra package:
+
+    pip install mergegi[sequana]
+
+It installs **snakemake** and **sequana_pipetools** and you have access to **sequana_mergegi** command.
+
+For developers:
+
+    git clone git@github.com:sequana/MergeGI.git
+    cd MergeGI
+    poetry install --all-extras
+    poetry shell
 
 ## Apptainers
 
 MergeGI is available as an apptainer image within the https://damona.readthedocs.io project. For example, the version 0.1.0 is available here:  https://sandbox.zenodo.org/record/1134857/files/mergegi_0.0.1.img  (60Mb).
 
-
 ## Overview
 
 The main goal of **MergeGI** is to select and merge the FastQ files generated by a MGI sequencer into a list of FastQ files directly usable for subsequent bioinformatics analysis. Why do we need to do this preprocessing ? 
@@ -48,7 +61,6 @@ Those 3 steps should be managed seemlessly by our tool given a sample sheet and
 
 ## General Usage and Examples
 
-
 The data structure expected by **MergeGI** is the expected output directoy of MGI runs:
 
     OutputFq/Flowcell/L01
@@ -102,6 +114,7 @@ mergegi --samplesheet samplesheet.csv --input-directory mgi_raw_data --output-di
 
 | Version  | Description  |  
 |----------|---
+| 0.2.0    | use poetry and add sequana_mergegi as extra dependencies |
 | 0.1.0    | simplify CI and use pyproject |
 | 0.0.0    | firs release  |