Merge pull request #37 from cokelaer/main

Refactorisation to use click

.github/workflows/apptainer.yml

@@ -8,7 +8,7 @@ on:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 * * SUN'
+    - cron: '0 0 20 * *'
 
 jobs:
   build-linux:

.github/workflows/main.yml

@@ -5,10 +5,11 @@ on:
     branches:
       - main
       - dev
+  workflow_dispatch:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 1 * *'
+    - cron: '0 0 20 * *'
 
 jobs:
   build-linux:

.github/workflows/pypi.yml

@@ -11,20 +11,20 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@main
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - 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@release/v1
       with:

README.rst

@@ -158,6 +158,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.19.0    * Refactorisation to use click
 0.18.1    * fastp multiqc regression. Fixed missing sample names by updating
             multiqc_config and adding sample names in the output filename
 0.18.0    * New plots in the HTML reports. Includes version of executables.

pyproject.toml

@@ -0,0 +1,52 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "sequana-rnaseq"
+version = "0.19.0"
+description = "A RNAseq pipeline from raw reads to feature counts"
+authors = ["Sequana Team"]
+license = "BSD-3"
+repository = "https://github.com/sequana/rnaseq"
+readme = "README.rst"
+keywords = ["snakemake, sequana, RNAseq, RNADiff, differential analysis"]
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Education",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: POSIX :: Linux",
+        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Scientific/Engineering :: Information Analysis",
+]
+
+packages = [
+    {include = "sequana_pipelines"}
+]
+
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+sequana = ">=0.16.0"
+sequana_pipetools = ">=0.16.2"
+click-completion = "^0.5.2"
+
+
+[tool.poetry.scripts]
+sequana_rnaseq = "sequana_pipelines.rnaseq.main:main"
+
+
+[tool.poetry.group.dev.dependencies]
+black = "^23.7.0"
+pytest = "^7.4.0"
+mock = "^5.1.0"
+pytest-mock = "^3.11.1"
+pytest-cov = "^4.1.0"
+

sequana_pipelines/rnaseq/config.yaml

@@ -7,7 +7,7 @@
 # If input_directory provided, use it otherwise if input_pattern provided,
 # use it, otherwise use input_samples.
 # ============================================================================
-sequana_wrappers: "v0.15.1"
+sequana_wrappers: "v23.12.5"
 
 input_directory:
 input_readtag: _R[12]_
@@ -25,6 +25,8 @@ apptainers:
   fastp: "https://zenodo.org/record/7319782/files/fastp_0.23.2.img"
   igvtools: "https://zenodo.org/record/7022635/files/igvtools_2.12.0.img"
   graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
+  multiqc: "https://zenodo.org/record/10205070/files/multiqc_1.16.0.img"
+
 
 # =========================================== Sections for the users
 
@@ -130,6 +132,8 @@ fastp:
     threads: 4
     disable_adapter_trimming: false
     disable_quality_filtering: false
+    resources:
+        mem: 8G
 
 #######################################################
 # Quality trimming software choice
@@ -390,6 +394,8 @@ multiqc:
     modules: ''
     input_directory: .
     config_file: multiqc_config.yaml
+    resources:
+        mem: 8G