update subset files for lgat fusions

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

Update create subset files module code to include fusions within LGAT fusion summary #830

What was your approach?

Add FGFR1--TACC1, MYB--QKI, BRAF to putative-oncogenic.tsv selection criteria for subsetting testing files.

• FGFR1--TACC1 is the only fusion in the 5' kinase in-frame dataframe which is rbound at the end
• MYB--QKI comes up in the non-kinase fusion dataframes
• BRAF fusions are in each of the remaining dataframes

What GitHub issue does your pull request address?

#834

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

Which areas should receive a particularly close look?

NA

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 and tested

Results

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

NA

What is your summary of the results?

NA

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]

Okay, I've uploaded a new version of the fusion file. We'll see if what's currently running on #830 works.

[jaclyn-taroni]

Code looks fine! We'll see if it sufficiently accounts for the changes in #830 before we merge this.

[jharenza]

Code looks fine! We'll see if it sufficiently accounts for the changes in #830 before we merge this.

I just pushed rerun for the circleCI tests because I think you updated this while the last tests were running and the data download step was probably pulling the older file, so the check did not pass.

[jharenza]

@jaclyn-taroni I just downloaded the testing file and the reason #830 is erroring out is that the additional columns added in #821 are not present. Can you subset from this file? Otherwise, it looks like the fusions I added are present with this script.

[jaclyn-taroni]

Talked about this offline, but wanted to record this here - since the notebook in #830 was using the file in analysis/fusion_filtering, the problem was not the file in CI but that fusion filtering came before the fusion summary module in #830. Moving the fusion summary module up in 9ffa3da resolved the issue.

[jaclyn-taroni]

This code to generate the CI files is not run in CI, so I'm going to go ahead and merge this.