Support for changing output directory (#7)

* Added support for changing output directory

* Update src/main/docker/RNApeg.sh

Co-authored-by: Andrew Thrasher <adthrasher@gmail.com>

* Extending functionality for selecting output directory including a default

* Update src/main/docker/RNApeg.sh

LGTM

Co-authored-by: Andrew Thrasher <adthrasher@gmail.com>

Co-authored-by: Andrew Thrasher <adthrasher@gmail.com>

src/main/docker/RNApeg.sh

@@ -11,10 +11,10 @@ REFFLAT=""
 REFGENE=""
 # optional refFlat for final gene annotation step only, if not specified REFFLAT
 # will be used.
-OUTPUT_DIR=/results
+OUTPUT_DIR=""
 
 usage() {
-    echo "RNApeg.sh [-h] -b bamfile -f fasta -r refflat [-rg refflat]"
+    echo "RNApeg.sh [-h] -b bamfile -f fasta -r refflat [-rg refflat] [-O output_dir]"
 }
 
 while [ ! -z "$1" ]; do
@@ -23,6 +23,7 @@ while [ ! -z "$1" ]; do
         -b) BAMFILE=$2; shift;;
         -r) REFFLAT=$2; shift;;
         -f) FASTA=$2; shift;;
+        -O) OUTPUT_DIR=$2; shift;;
         -rg) REFGENE=$2; shift;;
 	-version) echo 20191119; exit 1;;
 	*) echo "ERROR: unrecognized parameter $1"; usage; exit 1; shift;;
@@ -54,10 +55,6 @@ elif [[ ! -f $FASTA.fai ]]; then
     >&2 echo "ERROR: FASTA index file '$FASTA.fai' DNE; see samtools faidx command"
     usage
     exit 1
-elif [[ ! -d "$OUTPUT_DIR" ]]; then
-    usage
-    >&2 echo "ERROR: Output directory '$OUTPUT_DIR' does not exist; need mountpoint?"
-    exit 1
 fi
 
 if [[ -z "$REFGENE" ]]; then
@@ -78,6 +75,9 @@ fi
 ##################
 
 echo "[*] Running junction_extraction_wrapper.pl"
-junction_extraction_wrapper.pl -no-config -bam $BAMFILE -o $OUTPUT_DIR -fasta $FASTA -refflat $REFFLAT -refgene $REFGENE -now
-
-
+output_arg=
+if [[ -n "$OUTPUT_DIR" ]]; then
+    mkdir -p $OUTPUT_DIR
+    output_arg="-o $OUTPUT_DIR"
+fi
+    junction_extraction_wrapper.pl -no-config -bam $BAMFILE -fasta $FASTA -refflat $REFFLAT -refgene $REFGENE -now ${output_arg}