Option --unmapped does not run Bismark with --unmapped argument #595
Description
Description of the bug
The current code does not correctly use the argument "--un" to run Bismark to save unmapped reads when the pipeline parameter "--unmapped" is specified. Unmapped reads are therefore not saved when requested. Checking the .command.sh script in the relevant work folder, the argument is not included in the Bismark align command.
Command used and terminal output
Relevant files
No response
System information
No response