From ba83b38c591ee5b12d64ba324a8bb09cac1b0536 Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Fri, 27 Jul 2018 22:19:22 -0400
Subject: [PATCH] WIP

---
 pipes/WDL/workflows/tasks/tasks_demux.wdl | 31 +++++++++++++++++------
 1 file changed, 23 insertions(+), 8 deletions(-)

diff --git a/pipes/WDL/workflows/tasks/tasks_demux.wdl b/pipes/WDL/workflows/tasks/tasks_demux.wdl
index 8f791c82a..a295be258 100644
--- a/pipes/WDL/workflows/tasks/tasks_demux.wdl
+++ b/pipes/WDL/workflows/tasks/tasks_demux.wdl
@@ -68,16 +68,31 @@ task illumina_demux {
       ${flowcell_tgz} $FLOWCELL_DIR \
       --loglevel=DEBUG
 
-    echo "FLOWCELL_DIR: $FLOWCELL_DIR"
-    ls "$FLOWCELL_DIR"
-
     # full RunInfo.xml path
     RUNINFO_FILE="$(find $FLOWCELL_DIR -type f -maxdepth 3 -name RunInfo.xml | head -n 1)"
-    echo "RunInfo.xml: $RUNINFO_FILE"
-    cat "$RUNINFO_FILE"
-    cat "$RUNINFO_FILE"
-    cat "/opt/viral-ngs/source/docker/run_tile_count.sh"
-    total_tile_count=$("/opt/viral-ngs/source/docker/run_tile_count.sh $RUNINFO_FILE")
+    # Parse the lane count & run ID from RunInfo.xml file
+    lane_count=$(xmllint --xpath "string(//Run/FlowcellLayout/@LaneCount)" $RUNINFO_FILE)
+    if [ -z "$lane_count" ]; then
+        echo "Could not parse LaneCount from RunInfo.xml. Please check RunInfo.xml is properly formatted"
+    fi
+
+    surface_count=$(xmllint --xpath "string(//Run/FlowcellLayout/@SurfaceCount)" $RUNINFO_FILE)
+    if [ -z "$surface_count" ]; then
+        echo "Could not parse SurfaceCount from RunInfo.xml. Please check RunInfo.xml is properly formatted"
+    fi
+
+    swath_count=$(xmllint --xpath "string(//Run/FlowcellLayout/@SwathCount)" $RUNINFO_FILE)
+    if [ -z "$swath_count" ]; then
+        echo "Could not parse SwathCount from RunInfo.xml. Please check RunInfo.xml is properly formatted"
+    fi
+
+    tile_count=$(xmllint --xpath "string(//Run/FlowcellLayout/@TileCount)" $RUNINFO_FILE)
+    if [ -z "$tile_count" ]; then
+        echo "Could not parse TileCount from RunInfo.xml. Please check RunInfo.xml is properly formatted"
+    fi
+
+    # total data size more roughly tracks total tile count
+    total_tile_count=$((lane_count*surface_count*swath_count*tile_count))
 
     if [ "$total_tile_count" -le 50 ]; then
         echo "Detected $total_tile_count tiles, interpreting as MiSeq run."