adds shellcheck (#918)

* test

* test

* test

* remove precommit

* shellchecked

Author: jklugherz

.github/workflows/unit-tests.yml

@@ -34,6 +34,11 @@ jobs:
         run: ruff format --check v03_pipeline --diff
       - name: Check Ruff
         run: ruff . --output-format github
+      - name: Run ShellCheck
+        uses: ludeeus/action-shellcheck@master
+        with:
+          severity: error
+          scandir: './v03_pipeline/bin'
       - name: Unit Tests
         run: |
           export GRCH37_TO_GRCH38_LIFTOVER_REF_PATH=v03_pipeline/var/test/liftover/grch37_to_grch38.over.chain.gz

requirements-dev.in

@@ -5,3 +5,4 @@ nose-py3>=1.6.3 # bug in regular nose here: https://github.com/nose-devs/nose/is
 pip-tools>=6.12.3
 responses>=0.23.1
 ruff>=0.1.8
+shellcheck-py>=0.10.0

requirements-dev.txt

@@ -82,6 +82,8 @@ responses==0.24.1
     # via -r requirements-dev.in
 ruff==0.1.10
     # via -r requirements-dev.in
+shellcheck-py==0.10.0.1
+    # via -r requirements-dev.in
 six==1.16.0
     # via
     #   -c requirements.txt

v03_pipeline/bin/download_vep_reference_data.bash

@@ -13,7 +13,7 @@ case $REFERENCE_GENOME in
         # Raw data files copied from the bucket (https://console.cloud.google.com/storage/browser/dm_alphamissense;tab=objects?prefix=&forceOnObjectsSortingFiltering=false)
         # tabix -s 1 -b 2 -e 2 -f -S 1 AlphaMissense_hg38.tsv.gz
         'gs://seqr-reference-data/vep/GRCh38/AlphaMissense_hg38.tsv.*'
-        
+
         # Generated with:
         # curl -O ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz > Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
         # gzip -d Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
@@ -43,22 +43,22 @@ case $REFERENCE_GENOME in
     exit 1
 esac
 
-if [ -f $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME/_SUCCESS ]; then
+if [ -f "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS ]; then
    echo "Skipping download because already successful"
    exit 0;
 fi
 
-mkdir -p $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME;
-rm -rf $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME/*;
+mkdir -p "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME";
+rm -rf "${VEP_REFERENCE_DATASETS_DIR:?}"/"${REFERENCE_GENOME:?}"/*;
 
-for vep_reference_data_file in ${VEP_REFERENCE_DATA_FILES[@]}; do
+for vep_reference_data_file in "${VEP_REFERENCE_DATA_FILES[@]}"; do
     if  [[ $vep_reference_data_file == *.tar.gz ]]; then
-        echo "Downloading and extracting" $vep_reference_data_file;
-        gsutil cat $vep_reference_data_file | tar -xzf - -C $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME/ &
-    else 
-        echo "Downloading" $vep_reference_data_file;
-        gsutil cp $vep_reference_data_file $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME/ &
+        echo "Downloading and extracting" "$vep_reference_data_file";
+        gsutil cat "$vep_reference_data_file" | tar -xzf - -C "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ &
+    else
+        echo "Downloading" "$vep_reference_data_file";
+        gsutil cp "$vep_reference_data_file" "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/ &
     fi
 done;
 wait
-touch $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME/_SUCCESS
+touch "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME"/_SUCCESS

v03_pipeline/bin/vep

@@ -17,5 +17,5 @@ case $REFERENCE_GENOME in
 esac
 
 shift # Remove the REFERENCE_GENOME arg.
-docker run --platform linux/amd64 -i -v $VEP_REFERENCE_DATASETS_DIR/$REFERENCE_GENOME:/opt/vep/.vep/:ro $VEP_DOCKER_IMAGE:$REFERENCE_GENOME \
-  /opt/vep/src/ensembl-vep/vep $@
+docker run --platform linux/amd64 -i -v "$VEP_REFERENCE_DATASETS_DIR"/"$REFERENCE_GENOME":/opt/vep/.vep/:ro $VEP_DOCKER_IMAGE:"$REFERENCE_GENOME" \
+  /opt/vep/src/ensembl-vep/vep "$@"