PBTA Histologies v19 Part 2 of N: Update independent samples

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

Rna summary modules needed for subtyping need to be updated because BS_JXF8A2A6 is removed as per #862. In this PR I'm re-running the independent-samples module.

Module	Reason	Brief Description	output
independent-samples	BS_JXF8A2A6 is removed as per #862	Generates independent specimen lists for WGS/WXS samples updated in #795 and #797 and comment	results/independent-specimens.wgs.primary.tsv (included in data download) results/independent-specimens.wgs.primary-plus.tsv (included in data download) results/independent-specimens.wgswxs.primary.tsv (included in data download) results/independent-specimens.wgswxs.primary-plus.tsv (included in data download) results/independent-specimens.rnaseq.primary-plus-stranded.tsv(included in data download) results/independent-specimens.rnaseq.primary-plus-polya.tsv (included in data download)

What was your approach?

Just re-run as part of the scripts/run-for-subtyping.sh in kgaonkar6:v19-release in #1028
Then create a new branch for module specific review:
git checkout v19-release analyses/independent-samples/

What GitHub issue does your pull request address?

#867

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?

NA

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)?

tables

What is your summary of the results?

Some rna-seq sample selections have changed I believe because of the random selection

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.

[jashapiro]

LGTM! I guess the html was out of date or something about the files changed to make it parse more logical columns...

[kgaonkar6]

broad_composition was added back , kf_visibility is a new field in the v19 pbta-histologies-base.tsv file.
However, parent_aliquot_id might not be needed let me check with Jo Lynne.

[kgaonkar6]

Cols are updated in pbta-histologies-base.tsv to not include the new cols broad_composition and kf_visibility. The parent_aliquat_id is infact in v18 so it was accurately captured back.

[jashapiro]

LGTM