swithc channels bioconda and conda-forge

fixing cI

fixing cI

fixup! Merge pull request #8 from cokelaer/dev

fixup! Merge pull request #8 from cokelaer/dev

Author: cokelaer

.github/workflows/main.yml

@@ -38,18 +38,23 @@ jobs:
 
 
     - name: install package itself
+      shell: bash -l {0}
       run: |
-         pip install .
+        which pip
+        pip install .
 
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
         pip install coveralls pytest-cov pytest pytest-xdist
 
     - name: testing
+      shell: bash -l {0}
       run: |
         pytest -v --cov-report term-missing --cov=sequana_pipelines.fastqc
 
     - name: coveralls
+      shell: bash -l {0}
       run: |
         echo $COVERALLS_REPO_TOKEN
         coveralls --service=github

README.rst

@@ -132,6 +132,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.6.1     * pin sequana version to 1.4.4 to force usage of new fastqc module
+            to fix falco. Updated config documentation.
 1.6.0     * Fixed falco output error and use singularity containers
 1.5.0     * removed modules completely.
 1.4.2     * simplified pipeline (suppress setup and use existing wrapper)

environment.yml

@@ -1,8 +1,8 @@
 name: sequana_fastqc
 
 channels:
-- bioconda
 - conda-forge
+- bioconda
 - defaults
 - r
 

requirements.txt

@@ -1,2 +1,2 @@
-sequana>=0.14.3
+sequana>=0.14.4
 sequana_pipetools>=0.9.1

setup.py

@@ -5,7 +5,7 @@
 
 _MAJOR               = 1
 _MINOR               = 6
-_MICRO               = 0
+_MICRO               = 1
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)