add batch creation script

Author: ssadedin

scripts/create_batch.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+function usage() {
+      echo "Usage: $0 [options]"
+      echo
+      echo "-s <sample id> :   sample id"
+      echo "-d <dir>       :   directory containing pod5 files" 
+      echo ""
+      exit 0
+}
+
+while getopts "s:d:h" arg; do
+  case $arg in
+    s) # sample id
+      export sample_id=$OPTARG
+      ;;
+    d) # data
+      export data_path=$OPTARG
+      ;;
+     h | *) # Display help.
+         usage
+      ;;
+    :)
+      echo "Parameter -$OPTARG requires a positional argument"
+      exit 1
+      ;;
+  esac
+done
+
+if [ -z "$sample_id" ] || [ -z "$data_path" ];
+then
+    echo "Please specify sample and data path"
+
+    usage
+fi
+
+PREFIX=.
+
+if [ -e batches ];
+then
+	PREFIX=./batches
+fi
+
+BATCH_DIR=$PREFIX/${sample_id}
+
+mkdir $BATCH_DIR
+
+echo '
+samples:
+  - identifier: $sample_id
+    familyId: $sample_id
+    sex: female
+    inputs:
+        - $data_path
+    parents: null
+
+' | envsubst | tee $BATCH_DIR/samples.yaml
+
+
+echo
+echo "Done."
+echo
+echo "
+To run this:
+
+cd $BATCH_DIR
+
+# TODO: ADJUST SEX OF SAMPLES in samples.yaml
+
+bpipe run -p ANALYSIS_QUAL=hac --env ont_server /storage/warpy/src/pipeline.groovy -targets /storage/warpy/designs/WGS_REFFLAT_10_NOALT_38/WGS_REFFLAT_10_NOALT_38.bed -samples samples.yaml
+"