From c9675fda5b9e638b117dbd308383cf8e163fc761 Mon Sep 17 00:00:00 2001
From: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
Date: Fri, 3 Apr 2020 15:04:18 -0400
Subject: [PATCH] Comment out things downstream of TCGA snv callers

---
 .circleci/config.yml | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 44eb5a3f74..570593b703 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -200,21 +200,23 @@ jobs:
           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: 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: PBTA vs TCGA explore 
-          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/explore-tcga-pbta.Rmd', clean = TRUE)"
+      # - run:
+      #     name: PBTA vs TCGA explore 
+      #     command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/explore-tcga-pbta.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)"
+      # Retired analysis
+      # - 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)"
       
-      - run:
-          name: Lancet padded vs unpadded test
-          command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-padded-vs-unpadded.Rmd', clean = TRUE)"
+      # Retired analysis
+      # - run:
+      #     name: Lancet padded vs unpadded test
+      #     command: ./scripts/run_in_ci.sh Rscript -e "rmarkdown::render('analyses/snv-callers/lancet-wxs-tests/lancet-padded-vs-unpadded.Rmd', clean = TRUE)"
 
 
        # This analysis was a side concept question and no longer needs to be run.