optional bam storage

Author: Lennart Opitz

master/lib/CellRangerApp.rb

@@ -40,7 +40,7 @@ def initialize
     @params['bamStats'] = true
     @params['bamStats', 'description'] = 'Compute stats per cell from the bam file?'
     @params['keepBam'] = false
-    @params['bamStats', 'description'] = 'Keep bam file produced by CellRanger? Usually it is not neccessary for downstream analyses'
+    @params['keepBam', 'description'] = 'Keep bam file produced by CellRanger? Usually it is not neccessary for downstream analyses'
     @params['cmdOptions'] = ''
     @params['cmdOptions', 'description'] = 'specify the commandline options for CellRanger (e.g. --include-introns for single nuclei data); do not specify any option that is already covered by the dedicated input fields'
     @params['specialOptions'] = ''

master/lib/SpaceRangerApp.rb

@@ -31,6 +31,8 @@ def initialize
     Dir["/srv/GT/databases/10x_Probesets/Visium/*"].sort.select{|design| File.file?(design)}.each do |dir|
       @params['probesetFile'][File.basename(dir)] = File.basename(dir)
     end
+    @params['keepBam'] = false
+    @params['keepBam', 'description'] = 'Keep bam file produced by CellRanger? Usually it is not neccessary for downstream analyses'
     @params['cmdOptions'] = ''
     @params['cmdOptions', 'description'] = 'specify the commandline options for SpaceRanger; do not specify any option that is already covered by the dedicated input fields'
     @params['specialOptions'] = ''