diff --git a/master/lib/CellRangerApp.rb b/master/lib/CellRangerApp.rb index 664a7d5f..7a9edfb7 100644 --- a/master/lib/CellRangerApp.rb +++ b/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'] = '' diff --git a/master/lib/SpaceRangerApp.rb b/master/lib/SpaceRangerApp.rb index b5a32287..49c96a0e 100644 --- a/master/lib/SpaceRangerApp.rb +++ b/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'] = ''