Merge pull request #27 from cokelaer/main

Fixing CI action (apptainer)

Author: cokelaer

.github/workflows/apptainer.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
 
 
@@ -28,25 +28,20 @@ jobs:
         sudo rm -rf "$AGENT_TOOLSDIRECTORY"
     - name: install graphviz
       run: |
-        sudo apt-get install -y graphviz
+        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@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python 3.X
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v3
       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>3' 
-
     - name: Install dependencies
       run: |
         pip install .[testing]

environment.yml

@@ -1,4 +1,4 @@
-name: sequana_fastqc
+name: sequana_rnaseq
 
 channels:
 - conda-forge

sequana_pipelines/rnaseq/main.py

@@ -20,6 +20,7 @@
 import subprocess
 
 from sequana_pipetools.options import *
+from sequana_pipetools.options import before_pipeline
 from sequana_pipetools.misc import Colors
 from sequana_pipetools.info import sequana_epilog, sequana_prolog
 from sequana_pipetools import SequanaManager
@@ -164,8 +165,6 @@ def main(args=None):
         args = sys.argv
 
     # whatever needs to be called by all pipeline before the options parsing
-    from sequana_pipetools.options import before_pipeline
-
     before_pipeline(NAME)
 
     # option parsing including common epilog

sequana_pipelines/rnaseq/multiqc_config.yaml

@@ -28,7 +28,7 @@ intro_text: "Report summarising cleaning (cutadapt section) and mapping (stat/bo
 report_header_info:
    - Authors: '<a href="http://github.com/sequana/sequana">Sequana developers</a>'
    - Want to know more?: 'See the <a href="http://sequana.readthedocs.io" target="_blank">Sequana</a> and <a href="http://github.com/sequana/sequana_rnaseq/" target="_blank"> sequana_rnaseq pipeline</a> documentation.'
-   - Citations: 'If you used Sequanix, Sequana, Sequana_coverage tool, or any Sequana pipelines, please see <a href="http:/    /sequana.readthedocs.io">How to cite ?</a> section. In particular, if you use this report in a publication, please cite Sequana.'
+   - Citations: 'If you used Sequanix, Sequana, Sequana_coverage tool, or any Sequana pipelines, please see <a href="http://sequana.readthedocs.io">How to cite ?</a> section. In particular, if you use this report in a publication, please cite Sequana.'
    - Contact E-mail: ''
 #   - Project Type: 'Differential gene expression'