update MB SHH abridged output

[rjcorb]

Purpose/implementation Section

What scientific question is your analysis addressing?

This PR updates the molecular-subtyping-MB analysis module to remove non-relevant columns from abridged output generated by 05-subtype-mb-shh.R.

What was your approach?

Removed SHH_subtype column from mb_shh_molecular_subtypes.tsv, since molecular_subtype column contains complete information on SHH subtype classification.

What GitHub issue does your pull request address?

#599

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Results

What types of results are included (e.g., table, figure)?

What is your summary of the results?

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jharenza]

hi @rjcorb are the mutation calls being removed expected here?

[rjcorb]

@jharenza I reran the script and am still getting those changes to mb_shh_subtypes_w_molecular_data.tsv. For those biospecimen IDs that went from non-NA csq to NA, I don't see those IDs in either maf file. So I'm not sure how non-NA csqs were ever reported in those cases...

[jharenza]

I am not sure what is happening, but when I run this, I get the former result, with the non-NA results.

Line 109 for example:

[jharenza]

checks should all pass now, but can you double check re: my comments above - is your data linked to v15, not testing or something odd by chance?

[jharenza]

@rjcorb I just reran the full module and committed results so we are all set on this now

[jharenza]

module of interest passed checks