The BAM files generated during the pipeline execution are not being saved in the specified output folder. This results in missing output files that are crucial for further analysis.
Steps to Reproduce:
Run the pipeline and specify an output folder.
Check the output folder and observe that BAM files are missing.
Expected Behavior:
All BAM files should be saved in the specified output folder.
Tasks:
Investigate the file saving logic for BAM files.
Ensure that BAM files are correctly saved in the output folder.
Add tests to confirm the BAM files are saved as expected.
Description:
The BAM files generated during the pipeline execution are not being saved in the specified output folder. This results in missing output files that are crucial for further analysis.
Steps to Reproduce:
Expected Behavior:
All BAM files should be saved in the specified output folder.
Tasks: