The msisensorpro/pro module passes a scan list to pro -d and does not expose -i. Per ProUsage() in cpp/distribution.cpp L199-L206, -d has two modes:

1. msisensor-pro pro -d reference.list          -i 0.1 -t tumor.bam -o out
2. msisensor-pro pro -d reference.list_baseline        -t tumor.bam -o out

The wiki Best-Practices and the maintainer (xjtu-omics/msisensor-pro#77) recommend mode 2. The module silently runs mode 1 at the default threshold (0.1).

Requested changes:

1. Add msisensorpro/baseline module (missing piece between scan and pro).
2. Expose -i in msisensorpro/pro via ext.args.
3. Update meta.yml to document that -d accepts either a scan list or a baseline.

Happy to PR. Overlaps with #6007 and closed #6350.