TCGA Data Notebook Updates (#573)

* Add base notebook that is incorrect

* Re-run the TCGA consensus stuff and add it to the bash script

* Update TMB compare

* refresh notebook with new TMB

* Refreshy the notebooks

* Added a summary

* Rearrange order of CircleCI tests so the TMB has the data it needs

* Incorporate @jashapiro 's suggestions

* get rid of useless comment and replace with helpful info

* Update analyses/snv-callers/compare_snv_callers_plots-tcga.Rmd

Co-authored-by: jashapiro <josh.shapiro@ccdatalab.org>

.circleci/config.yml

@@ -108,10 +108,6 @@ jobs:
           name: Mutational Signatures 
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/mutational-signatures/mutational_signatures.Rmd', clean = TRUE)" 
 
-      - run:
-          name: Tumor mutation burden with TCGA
-          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/tmb-compare-tcga/compare-tmb.Rmd', clean = TRUE)"
-
       - run:
           name: Chromosomal instability breakpoints
           command: OPENPBTA_TESTING=1 ./scripts/run_in_ci.sh bash analyses/chromosomal-instability/run_breakpoint_analysis.sh
@@ -180,7 +176,11 @@ jobs:
       - run:
           name: SNV Caller Analysis 
           command: OPENPBTA_VAF_CUTOFF=0.5 ./scripts/run_in_ci.sh bash analyses/snv-callers/run_caller_consensus_analysis-pbta.sh
-
+
+      - run:
+          name: Tumor mutation burden with TCGA
+          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/tmb-compare-tcga/compare-tmb.Rmd', clean = TRUE)"
+
       - run:
           name: Lancet WXS vs WGS test
           command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-paired-WXS-WGS.Rmd', clean = TRUE)"