Comment out things downstream of TCGA snv callers

AlexsLemonade · Apr 3, 2020 · c9675fd · c9675fd
1 parent bca7c85
commit c9675fd
Showing 1 changed file with 14 additions and 12 deletions.
diff --git 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.