add missing dep

Author: lpantano

.github/workflows/python-package-conda.yml

@@ -37,8 +37,10 @@ jobs:
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        #flake8 . --count  --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         conda install pytest
+        python setup.py develop
         pytest

environment.yml

@@ -2,5 +2,6 @@ dependencies:
   - python=3.11
   - bioconda::pysam
   - bioconda::pybedtools
+  - bioconda::samtools=1.21
   - conda-forge::pandas
   - conda-forge::biopython=1.83