update yaml, run cluster only locally

.github/workflows/run_analysis.yml

@@ -98,7 +98,8 @@ jobs:
 
  - name: Molecular Subtyping - PB
  entrypoint: molecular-subtyping-PB/run-molecular-subtyping-PB.sh
-
+ openpbta_subset: 0
+
  - name: Molecular Subtyping - NBL
  entrypoint: molecular-subtyping-NBL/run-molecular-subtyping-NBL.sh
 

analyses/molecular-subtyping-PB/run-molecular-subtyping-PB.sh

@@ -10,8 +10,7 @@ script_directory="$(perl -e 'use File::Basename;
  print dirname(abs_path(@ARGV[0]));' -- "$0")"
 cd "$script_directory" || exit
 
-# This option controls whether on not the step that generates the HGG only
-# files gets run -- it will be turned off in CI
+# This will be turned off in CI
 SUBSET=${OPENPBTA_SUBSET:-1}
 
 scratch_path="../../scratch/"
@@ -27,22 +26,23 @@ Rscript -e "rmarkdown::render('01-molecular-subtype-pineoblastoma.Rmd', clean =
 
 
 if [ "$SUBSET" -gt "0" ]; then
- echo "classify SHH samples into alpha, beta, delta, gamma"
- Rscript --vanilla 05-subtype-mb-shh.R
-
  echo "check whether methylation files exist"
  URL="https://d3b-openaccess-us-east-1-prd-pbta.s3.amazonaws.com/open-targets"
  RELEASE="v15"
  BETA="methyl-beta-values.rds"
  if [ -f "${data_dir}/${BETA}" ]; then
  echo "${BETA} exists, skip downloading"
- else 
+ echo "run pineoblastoma clustering"
+ # add umap
+ Rscript -e "rmarkdown::render('02-pineoblastoma-umap.Rmd', clean = TRUE)"
+ else 
  echo "${BETA} does not exist, downloading..."
  wget ${URL}/${RELEASE}/${BETA} -P ${data_dir}/${RELEASE}/
  cd ${data_dir}
  ln -sfn ${RELEASE}/${BETA} ./${BETA}
  cd ../analyses/molecular-subtyping-MB
+ echo "run pineoblastoma clustering"
+ # add umap
+ Rscript -e "rmarkdown::render('02-pineoblastoma-umap.Rmd', clean = TRUE)"
  fi
-
-# add umap
-Rscript -e "rmarkdown::render('02-pineoblastoma-umap.Rmd', clean = TRUE)"
+