Merge pull request #4 from cokelaer/main

add apptainer CI

.github/workflows/apptainer.yml

@@ -0,0 +1,57 @@
+name: Apptainer Run
+
+on:
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches-ignore: []
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+      matrix:
+        python: [3.8, 3.9, '3.10']
+      fail-fast: false
+
+
+    steps:
+
+    - name: precleanup
+      run: |
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+    - name: install graphviz
+      run: |
+        sudo apt update
+        sudo apt-get install -y graphviz software-properties-common
+        sudo add-apt-repository -y ppa:apptainer/ppa
+        sudo apt update
+        sudo apt install -y apptainer
+
+    - name: checkout git repo
+      uses: actions/checkout@v3
+
+    - name: Set up Python 3.X
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python }}
+
+    - name: Install dependencies
+      run: |
+        pip install .[testing]
+
+    - name: install package itself
+      run: |
+         pip install .
+
+    - name: testing
+      run: |
+        sequana_revcomp --input-directory test/data/  --use-apptainer && cd revcomp && sh revcomp.sh
+
+

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.7, 3.8, 3.9]
+        python: [3.8, 3.9, '3.10']
       fail-fast: false
 
     steps:

README.rst

@@ -10,6 +10,9 @@
    :target: https://github.com/sequana/revcomp/actions/workflows    
 
 
+.. image:: https://img.shields.io/badge/python-3.8%20%7C%203.9%20%7C3.10-blue.svg
+    :target: https://pypi.python.org/pypi/sequana
+    :alt: Python 3.8 | 3.9 | 3.10
 
 This is is the **revcomp** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
 
@@ -18,29 +21,24 @@ This is is the **revcomp** pipeline from the `Sequana <https://sequana.readthedo
 :Output: A set of reverse completed files
 :Status: production
 :Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
-:Authors: Thomas Cokelaer
+
 
 
 
 
 Installation
 ~~~~~~~~~~~~
 
-You must install Sequana first::
-
-    pip install sequana
-
-Then, just install this package::
-
-    pip install sequana_revcomp
+If you already have all requirements, you can install the packages using pip::
 
+    pip install sequana_mapper --upgrade
 
 Usage
 ~~~~~
 
 ::
 
-    sequana_pipelines_revcomp --input-directory DATAPATH 
+    sequana_revcomp --input-directory DATAPATH 
 
 This creates a directory with the pipeline and configuration file. You will then need 
 to execute the pipeline::
@@ -52,7 +50,8 @@ to execute the pipeline::
 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 revcomp.rules -c config.yaml --cores 4 --stats stats.txt
+    snakemake -s revcomp.rules -c config.yaml --cores 4 \
+        --wrapper-prefix https://raw.githubusercontent.com/sequana/sequana-wrappers/
 
 Or use `sequanix <https://sequana.readthedocs.io/en/main/sequanix.html>`_ interface.
 

requirements.txt

@@ -1,2 +1,2 @@
-sequana>=0.8.4
-sequana_pipetools>=0.2.1
+sequana>=0.15.1
+sequana_pipetools>=0.12.4

sequana_pipelines/revcomp/config.yaml

@@ -12,6 +12,9 @@ input_directory: ''
 input_readtag: _R[12]_
 input_pattern: '*.fastq.gz'
 
+apptainers:
+  seqtk: "https://zenodo.org/record/5729951/files/seqtk_1.3.0.img" 
+
 
 ##############################################################################
 # Revcomp section

sequana_pipelines/revcomp/revcomp.rules

@@ -35,7 +35,7 @@ rule revcomp:
     log:
         temp("logs/{sample}.logs")
     container:
-        "https://zenodo.org/record/5729951/files/seqtk_1.3.0.img" 
+        config["apptainers"]["seqtk"]
     shell:
         """
         # -k means keep original data

sequana_pipelines/revcomp/schema.yaml

@@ -19,4 +19,6 @@ mapping:
                 type: str
             "threads":
                 type: int
+    "apptainers":
+        type: any
 

setup.py

@@ -5,8 +5,8 @@
 from setuptools.command.install import install
 import subprocess
 
-_MAJOR               = 0
-_MINOR               = 9
+_MAJOR               = 1
+_MINOR               = 0
 _MICRO               = 0
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)
@@ -27,9 +27,9 @@
           'Intended Audience :: Science/Research',
           'License :: OSI Approved :: BSD License',
           'Operating System :: OS Independent',
-          'Programming Language :: Python :: 3.7',
           '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',