add v18 release

[jharenza]

Purpose/implementation Section

What scientific question is your analysis addressing?

V18 data release

What was your approach?

• changes:
  • Add RNA independent specimen lists from #795 and #797
  • Update DNA independent specimen lists per comment here
  • Add LGAT fusion summary file from #808 and #830
  • Update fusion files per comment here
• Add kinase domain and reciprocal information to pbta-fusion-putative-oncogenic.tsv per #812 and #816 and #821
  • Add 8 rRNA-depleted, total stranded RNA-Seq for tumors which previously had polyA sequencing performed: BS_FXJY0MNH, BS_KABQQA0T, BS_D7XRFE0R, BS_SHJA4MR0, BS_HE0WJRW6, BS_8QB4S4VA, BS_FN07P04C, BS_SB12W1XT per #749
  • Update pbta-histologies.tsv:
    • Add new RNA samples above
    • Pull latest clinical data
    • Add extent of tumor resection per comment
    • Rerun molecular subtyping modules to date

What GitHub issue does your pull request address?

#750

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?

no

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.

Data Release Checklist

• Is the table in doc/data-file-descriptions.md up to date?
• Is doc/data-format.md up to date?
• Is doc/release-notes.md up to date?
• Is download-data.sh up to date?
• Was download-data.sh tested and did it complete without error?

[jharenza]

note: will need to update release notes to include both histologies files per #858. cc @kgaonkar6

[jharenza]

Just leaving a note - all files except for pbta-histologies.tsv are updated on S3 and download works. We have added pbta-histologies-base.tsv per this issue and are currently in the stage of rerunning molecular subtyping for the new histologies file.

[jharenza]

Wanted to docunent on this PR some intermediate QC here:

• QC on the RNA-Seq merge files
• pbta-histologies-base.tsv construction to include:
  • BIXU-generated fields from v17
  • Updated metadata for new RNA-Seq samples
  • broad_histology and short_histology mapping from pathology_diagnosis and pathology_free_text_diagnosis
  • CNS_region logic per Proposed Analysis: Add CNS_region mapping in histologies file to OpenPBTA analyses #838

[kgaonkar6]

@jharenza @jaclyn-taroni @cansavvy the following output files generated as part of base subtyping run are uploaded in s3. Details of other modules re-run are described in #861

Module	Reason	Brief Description	output
collapse-rnaseq	adding 8 samples #749 and used in subtyping	Collapses RSEM FPKM matrices such that gene symbols are de-duplicated.	results/pbta-gene-expression-rsem-fpkm-collapsed.polya.rds (included in data download; too large for tracking via GitHub) results/pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds (included in data download; too large for tracking via GitHub)
fusion_filtering	adding 8 samples #749 and used in subtyping	Standardizes, filters, and prioritizes fusion calls updated in #808 and #830	results/pbta-fusion-putative-oncogenic.tsv(included in data download) results/pbta-fusion-recurrent-fusion-byhistology.tsv (included in data download) results/pbta-fusion-recurrent-fusion-bysample.tsv (included in data download) results/fusion_summary_lgat_foi.tsv (included in data download)
fusion-summary	adding 8 samples #749 and used in subtyping	Generate summary tables from fusion files updated in #812 and #816 and #821 and comment	results/fusion_summary_embryonal_foi.tsv (included in data download) results/fusion_summary_ependymoma_foi.tsv (included in data download) results/fusion_summary_ewings_foi.tsv
independent-samples	adding 8 samples #749 and used in subtyping	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)
molecular-subtyping-integrate	to add subtyping to base histology	Add molecular subtype information to base histology	results/pbta-histologies.tsv(included in data download)

[jaclyn-taroni]

I think we're ready to merge!