Update to handle capture data

[rdmorin]

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[mattssca]

Good updates, see comments for suggestions and questions. For me, I got an error when testing get_ssm_by_sample related to the maf path (saying the file does not exist). I updated my working directory but still got a similar error. For testing, I cloned this branch and ran the functions after loading this specific gamblr branch. This is how I ran the previously mentioned function ssm = get_ssm_by_sample(this_sample_id = "BLGSP-71-06-00001-01A-11D") while cd onto the cloned gamblr branch.

[mattssca]

Maybe add overwrite option (default to FALSE?) to wflow_git_config()

[rdmorin]

I think I understand what causes this. Which "flavour" did you specify? Presumably just the default. Can you please retry with flavour="clustered"

[mattssca]

Indeed!

After updating this line to if(this_pairing_status == "unmatched") and flavour = "clustered" the function runs the intended way.

#60 (comment)

[rdmorin]

Unfortunately I can't finalize and test the new version of this function without the final deblacklisted MAFs.

[mattssca]

Adding descriptions of parameters, even though rather self-explenatory (to have consistent documentation generated).

[mattssca]

nothing

[rdmorin]

I think this is good to go