Bam file could have two different file extensions depending on the tools. Given bam file test.bam,
- test.bam.bai secondaryFiles = [.bai]
- test.bai secondaryFiles = [^.bai]
For a flow to work with both kinds of bam inputs, how to set the secondaryFiles?
Since secondaryFiles items must be present, it is not possible to set the secondaryFiles to handle bam input from any bam index convention.