Fix syntax.

scripts/split_study.sh

@@ -44,31 +44,32 @@ main(){
     # query GUDMAP/RBK for study RID
     echo "curl --location --request GET 'https://www.gudmap.org/ermrest/catalog/2/entity/RNASeq:Replicate/Study_RID="${rid}"'" | bash > $rid\_studyRID.json
 
-  # extract replicate RIDs
+    # extract replicate RIDs
 
-  python3 ./scripts/split_study.py -s $rid
+    python3 ./scripts/split_study.py -s $rid
 
-  # cleanup study RID files
-  rm $rid\_studyRID.json
+    # cleanup study RID files
+    rm $rid\_studyRID.json
 
-  # make dir for study
-  mkdir $out/$rid
-  mv $rid\_studyRID.csv $out/$rid
-  cd $out/$rid
+    # make dir for study
+    mkdir $out/$rid
+    mv $rid\_studyRID.csv $out/$rid
+    cd $out/$rid
 
-  # download version of RNA-seq pipelne
-  existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag})
+    # download version of RNA-seq pipelne
+    existed_in_remote=$( git ls-remote --tags git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git ${tag})
 
-  if [[ -z ${existed_in_remote} ]]; then
-      echo "The tag ${tag} doesn't exist."
-      exit 1
-  fi
+    if [[ -z ${existed_in_remote} ]]; then
+        echo "The tag ${tag} doesn't exist."
+        exit 1
+    fi
+
+    git clone -b $tag --depth 1 git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git
+    cd rna-seq
 
-  git clone -b $tag --depth 1 git@git.biohpc.swmed.edu:gudmap_rbk/rna-seq.git
-  cd rna-seq
+    # run pipeline on replicate RIDs in parallel
+    while read repRID; do echo ${repRID}; sleep 30; done < "../${rid}_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email ${email} -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
 
-  # run pipeline on replicate RIDs in parallel
-  while read repRID; do echo ${repRID}; sleep 30; done < "../${rid}_studyRID.csv" | xargs -P 5 -I {} nextflow -q run workflow/rna-seq.nf --repRID {} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email ${email} -with-report ./output/{}_report.html -with-timeline ./output/{}_timeline.html
 }
 
 main "$@"