run_deeptrio.py: help says --sample_name_child is optional, but is actually required

[milenovic]

There appears to be a mismatch between the CLI/help text and the actual validation logic in run_deeptrio.py.

The help text for --sample_name_child says:

Sample name to use for the child sample. If not specified, it is inferred from the header information from --reads_child.

However, when I run DeepTrio without --sample_name_child, the wrapper exits immediately with:

--sample_name_child is required.

This is enforced in the wrapper’s required-flag validation logic in run_deeptrio.py, lines 1262–1272

In that block, sample_name_child is included in the list of required flags, causing the script to exit if it is missing.

[lucasbrambrink]

You're absolutely right! Thank you for pointing that out. I've created a ticket internally for us to fix these flags and align them with expectations and documentation.