Add OS_months to final ATRT molecular subtyping table

[cbethell]

Purpose/implementation Section

To add OS_months column to final ATRT molecular subtyping table.

What scientific question is your analysis addressing?

The molecular subtyping of ATRT samples in the OpenPBTA dataset.

What was your approach?

Per #244 (comment), I used the OS_days column in the data/pbta-histologies.tsv file to calculate the values for the new OS_months column.

What GitHub issue does your pull request address?

This PR addresses issue #244.

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

Which areas should receive a particularly close look?

Does this conversion from days to months appear to be correct?

Is there anything that you want to discuss further?

@jharenza does this satisfy your request?

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

Yes, this PR is ready for review.

Results

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

The final results file analyses/molecular-subtyping-ATRT/results/ATRT_molecular_subtypes.tsv has been updated to include the new OS_months column.

The updated html output can be viewed here.

Note: I reran the molecular-subtyping-ATRT module with the data from v13 release.

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.

[jaclyn-taroni]

[jharenza]

that was super quick, yes, thanks!