Changeset 5476

Timestamp:

Jun 10, 2019, 9:50:39 AM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1142: Create MIPs flow cell and start sequencing

Updated the hiseq_status.sh script so that will check if a file or folder exists before trying to use it.

File:

• other/pipeline/trunk/hiseq_status.sh (modified) (2 diffs)

other/pipeline/trunk/hiseq_status.sh

@@ -59 +59 @@
 # use this for progress reporting
 RUN_PARAMETERS=${DATA_FOLDER}/runParameters.xml
-RUN_INFO=${DATA_FOLDER}/RunInfo.xml
 if [ -f "${RUN_PARAMETERS}" ]; then
   echo "RunParameters: `date +"${DATE_FORMAT}" -r "${RUN_PARAMETERS}"`"
-  echo "BclCount: `find "${DATA_FOLDER}" -type f -name *.bcl | wc -l`"
-  echo "LaneCount: `grep -o 'LaneCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
-  echo "SurfaceCount: `grep -o 'SurfaceCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
-  echo "SwathCount: `grep -o 'SwathCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
-  echo "TileCount: `grep -o 'TileCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
   echo "Read1: `grep '<Read1>' "${RUN_PARAMETERS}" | cut -d '>' -f 2 | cut -d '<' -f 1`"
   echo "Read2: `grep '<Read2>' "${RUN_PARAMETERS}" | cut -d '>' -f 2 | cut -d '<' -f 1`"
@@ -74 +68 @@
 fi
 
+# Count number of BCL files which gives us information about
+# the progress of the sequencing
+BCL_FOLDER=${DATA_FOLDER}/Data/Intensities/BaseCalls
+if [ -d "${BCL_FOLDER}" ]; then
+  echo "BclCount: `find "${BCL_FOLDER}" -type f -name *.bcl | wc -l`"
+fi
+
+# RunInfo.xml contains information about the layout of the flowcell
+# which we need to be able to compare the number of BCL files
+RUN_INFO=${DATA_FOLDER}/RunInfo.xml
+if [ -f "${RUN_PARAMETERS}" ]; then
+  echo "LaneCount: `grep -o 'LaneCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
+  echo "SurfaceCount: `grep -o 'SurfaceCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
+  echo "SwathCount: `grep -o 'SwathCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
+  echo "TileCount: `grep -o 'TileCount="[^"]*"' "${RUN_INFO}" | cut -d '"' -f 2`"
+fi
+
+
+
 # RTAComplete.txt is created when everything is complete
 # This becomes the end date of the job and should trigger