fixing logic for existing downloads in bash script #88

haniffalab · Feb 4, 2025 · 833121c · 833121c
1 parent 75f1409
commit 833121c
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/bin/irods/iget-cellranger/submit.sh b/bin/irods/iget-cellranger/submit.sh
@@ -90,7 +90,7 @@ OUTPUT_DIR="${TEAM_SAMPLE_DATA_DIR}/\$SAMPLE/cellranger"
 # check if cellranger outputs for $SAMPLE have already been pulled, exit
 #OUTS=\$(sed 's|.*/||' \$OUTPUT_DIR/irods_path.csv)
 
-[ -d "$OUTPUT_DIR/$OUTS" ]
+[ -d "$OUTPUT_DIR/$OUTS/*GRCh38*" ]
 if [ -d "\$OUTPUT_DIR/\$OUTS" ]; then
     echo "Output directory '\$OUTPUT_DIR' already contains cellranger outputs from iRODS. Exiting"
     exit 2