Undo cancer_group manual override for select sample_ID as per OPC_566

[sangeetashukla]

Purpose/implementation Section

Fix cancer_group and subtype mismatch for BS_YZD4SSMA

What scientific question is your analysis addressing?

There was a manual hard-coding of cancer_group for a specific sample_id. This caused the cancer_group and subtype mismatch. I investigated the source to fix the mismatch.

What was your approach?

Review the molecular-subtyping-integrate module to investigate the values in the input data sources
Review the KF_BS 'BS_YZD4SSMA' to locate manual override.
Undo such hardcoding, and review the result files to confirm cancer_group and subtype match.

What GitHub issue does your pull request address?

Issue 566

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

Which areas should receive a particularly close look?

Please review the result files to confirm the data for 'BS_YZD4SSMA' is acceptable.

Is there anything that you want to discuss further?

No.

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

Yes.

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]

ahh, this was a bit complicated because there is an upstream issue where two samples for this patient is are the database as being from two different patients - i changed what was needed here to make sure we capture both samples but for reference: https://d3b.atlassian.net/browse/D3B-95

[jharenza]

merging since the relevant module passed