MSI check not completely ok #290
Description
Description of the bug
I ran the pipeline and got the following warning:
WARN: MSI samples were found, but no MSI baseline file was provided. Please provide a baseline file using the '--msi_baseline' parameter. Skipping MSI analysis...
yet the docs specify
msi OPTIONAL - Set this to true when MSI calling should be performed on this sample. MSI calling is only done when a CRAM file is supplied and a baseline file has been provided via the --msi_baseline parameter. (By default this option is false)
and my samplesheet only contains
sample,family,cram,crai
Command used and terminal output
Relevant files
No response
System information
No response