v18 CI files

[jaclyn-taroni]

We need to update the CI files to reflect the v18 release. The v18 release makes the following changes (quoting from #857):

• 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

Known changes required to create-subset-files

• We need copy the pbta-histologies-base.tsv file in the shell script like we do for pbta-histologies.tsv

OpenPBTA-analysis/analyses/create-subset-files/create_subset_files.sh

Line 56 in 83d3e1c

cp $FULL_DIRECTORY/pbta-histologies.tsv $SUBSET_DIRECTORY

• Update the release

OpenPBTA-analysis/analyses/create-subset-files/create_subset_files.sh

Line 10 in 83d3e1c

RELEASE=${RELEASE:-release-v17-20200908}

Potential "gotchas"

I think some of the v18 file additions, which usually break things, should be covered by the existing code. I'm including this section just in case there's anything unexpected.

• Add RNA independent specimen lists from #795 and [adding function to find independent rna samples #797](Make it such that sample distribution scripts can be run from anywhere in project #79

These files are named independent-specimens.rnaseq.primary-plus-polya.tsv and independent-specimens.rnaseq.primary-plus-stranded.tsv according to #857. That should be covered by:

OpenPBTA-analysis/analyses/create-subset-files/create_subset_files.sh

Line 66 in 83d3e1c

cp $FULL_DIRECTORY/independent-specimens*.tsv $SUBSET_DIRECTORY

• Add LGAT fusion summary file from #808 and #830

This file is called fusion_summary_lgat_foi.tsv according to #857. That should be covered by:

OpenPBTA-analysis/analyses/create-subset-files/create_subset_files.sh

Line 85 in 83d3e1c

cp $FULL_DIRECTORY/fusion_summary* $SUBSET_DIRECTORY

Next steps

These steps are adapted from #670

1. Start AWS instance with 128 GB RAM
2. Clone OpenPBTA-analysis
3. Create a new branch off of jharenza:v18-files called v18-ci
4. Update analyses/create-subset-files/create_subset_files.sh as outlined above ☝️
5. Run bash analyses/create-subset-files/create_subset_files.sh
6. Commit the biospecimen RDS file to v18-ci branch.
7. Zip up the subset files in data/testing/release-v18-20201123/ to testing_v18.zip
8. Download testing_v18.zip
9. File a pull request from v18-ci