Merge de4f76d into 71fe819

.github/workflows/main.yml

@@ -3,17 +3,21 @@ name: Tests
 on:
   push:
     branches:
-      - master
+      - main
+      - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
+  schedule:
+    - cron: '0 0 30 * *'
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.7,3.8,3.9]
+        python: [3.8,3.9,'3.10']
       fail-fast: false
 
 
@@ -26,36 +30,33 @@ jobs:
     - name: checkout git repo
       uses: actions/checkout@v2
 
-    - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+    - name: conda/mamba
+      uses: mamba-org/setup-micromamba@v1
       with:
-        python-version: ${{ matrix.python }}
+          micromamba-version: '1.3.1-0'
+          environment-file: environment.yml
+          create-args: |
+            python=${{ matrix.python }}
+          cache-environment: true
+          cache-downloads: true
 
-    - 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
-        conda update ruamel_yaml
-
-    - name: conda
+    - name: install package itself
+      shell: bash -el {0}
       run: |
-        conda install -c conda-forge mamba --quiet
-        mamba install -c bioconda -c conda-forge --quiet -y fastqc  bwa samtools bamtools sambamba pigz
-
+        pip install .
 
     - name: Install dependencies
+      shell: bash -el {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
-    - name: install package itself
-      run: |
-         pip install .
-
     - name: testing
+      shell: bash -el {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.quality_control
 
     - name: coveralls
+      shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github

.github/workflows/pypi.yml

@@ -8,32 +8,32 @@ on:
 jobs:
   build-n-publish:
     name: Build and publish to PyPI and TestPyPI
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@master
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@main
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
-    - name: Install package
+    - name: Install package 
       run: |
-          pip install build
+          pip install build poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
-          python setup.py sdist
-
+          poetry build
+ 
     - name: Publish distribution to Test PyPI
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.TEST_PYPI_API_TOKEN }}
         repository_url: https://test.pypi.org/legacy/
     - name: Publish distribution to PyPI
       if: startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@master
+      uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

.pre-commit-config.yaml

@@ -0,0 +1,33 @@
+
+files: '\.(py|rst|sh)$'
+fail_fast: false
+
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    #-   id: check-executables-have-shebangs
+    -   id: check-ast
+
+-   repo: https://github.com/pycqa/flake8
+    rev: 6.1.0
+    hooks:
+    -   id: flake8
+        args: ["-j8", "--ignore=E203,E501,W503,E722", "--max-line-length=120", "--exit-zero"]
+
+-   repo: https://github.com/psf/black
+    rev: 22.10.0
+    hooks:
+    -   id: black
+        args: ["--line-length=120"]
+        exclude: E501
+
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black"] # solves conflicts between black and isort
+

README.rst

@@ -7,7 +7,7 @@
     :alt: JOSS (journal of open source software) DOI
 
 .. image:: https://github.com/sequana/quality_control/actions/workflows/main.yml/badge.svg
-   :target: https://github.com/sequana/quality_control/actions/workflows    
+   :target: https://github.com/sequana/quality_control/actions/workflows
 
 
 This pipeline is not maintained anymore but should be functional. It is a short-read quality control pipeline
@@ -39,15 +39,15 @@ Usage
 ::
 
     sequana_quality_control --help
-    sequana_quality_control --input-directory DATAPATH 
+    sequana_quality_control --input-directory DATAPATH
 
-This creates a directory with the pipeline and configuration file. You will then need 
+This creates a directory with the pipeline and configuration file. You will then need
 to execute the pipeline::
 
     cd quality_control
     sh quality_control.sh  # for a local run
 
-This launch a snakemake pipeline. If you are familiar with snakemake, you can 
+This launch a snakemake pipeline. If you are familiar with snakemake, you can
 retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
 
     snakemake -s quality_control.rules -c config.yaml --cores 4 --stats stats.txt
@@ -61,8 +61,6 @@ This pipelines requires the following executable(s):
 
 - fastqc
 - bwa
-- kraken2 (optional)
-- krona (optional)
 - sambamba
 - samtools
 - pigz
@@ -74,15 +72,15 @@ This pipelines requires the following executable(s):
 Details
 ~~~~~~~
 
-This pipeline runs **quality_control** in parallel on the input fastq files (paired or not). 
+This pipeline runs **quality_control** in parallel on the input fastq files (paired or not).
 A brief sequana summary report is also produced.
 
 
 Rules and configuration details
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_quality_control/master/sequana_pipelines/quality_control/config.yaml>`_
-to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
+to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
 
 ChangeLog
 ~~~~~~~~~
@@ -91,9 +89,11 @@ ChangeLog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
-0.10.0    * add missing MANIFEST 
+0.11.0    * switch to click, pyproject. remove kraken (see multitax pipeline
+            instead)
+0.10.0    * add missing MANIFEST
 0.9.0     * remove design_file for cutadapt to reflect changes in
-            sequana 0.12.0 
+            sequana 0.12.0
           * update kraken rules to use a kraken2 version
           * Update to use new sequana framework (0.12)
           * added CI action

environment.yml

@@ -0,0 +1,19 @@
+name: mapper
+
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+
+dependencies:
+  - bwa
+  - samtools
+  - pigz
+  - fastqc
+  - sambamba
+  - pip:
+    - sequana
+    - cutadapt
+    - atropos
+
+