extend app to work with SC and Spatial data

master/lib/SeuratCompareApp.rb

@@ -0,0 +1,60 @@
+#!/usr/bin/env ruby
+# encoding: utf-8
+Version = '20210702-145619'
+
+require 'sushi_fabric'
+require_relative 'global_variables'
+include GlobalVariables
+
+class SeuratCompareApp < SushiFabric::SushiApp
+  def initialize
+    super
+    @name = 'SeuratCompare'
+    @params['process_mode'] = 'DATASET'
+    @analysis_category = 'Differential_Expression'
+    @description =<<-EOS
+    Empirical analysis of digital gene expression data in R<br/>
+<a href='https://bioconductor.org/packages/release/bioc/html/DifferentialState.html'>DifferentialState</a><br/>
+    EOS
+    @required_columns = ['Name', 'Condition']
+    @required_params = ['grouping', 'sampleGroup', 'refGroup']
+    # optional params
+    @params['cores'] = '4'
+    @params['ram'] = '30'
+    @params['scratch'] = '50'
+    @params['DE.method'] = ['wilcox', 'LR']
+    @params['DE.method', 'description'] = "Method to be used when calculating differentially expressed genes between conditions."
+    @params['DE.regress'] = ['Batch', 'CellCycle']
+    @params['DE.regress','multi_selection'] = true
+    @params['DE.regress', 'description'] = "Variables to regress when calculating differentially expressed genes. Only used with the LR method."
+    @params['grouping'] = '' ## Note: this will be a selector defined by Factor tagged column
+    @params['sampleGroup'] = '' ## Note: this will be a selector defined by Factor tagged column
+    @params['sampleGroup', 'description'] = 'sampleGroup should be different from refGroup'
+    @params['refGroup'] = '' ## Note: this will be a selector defined by Factor tagged column
+    @params['refGroup', 'description'] = 'refGroup should be different from sampleGroup'
+    @params['mail'] = ""
+    @params['Rversion'] = ["Dev/R/4.1.2", "Dev/R/4.1.0", "Dev/R/4.0.4", "Dev/R/4.0.3"]
+  end
+   def preprocess
+    @random_string = (1..12).map{[*('a'..'z')].sample}.join
+  end
+  def next_dataset
+    @comparison = "#{@params['sampleGroup']}--over--#{@params['refGroup']}"
+    @params['comparison'] = @comparison
+    @params['name'] = @comparison
+    report_file = File.join(@result_dir, "#{@params['comparison']}")
+    report_link = File.join(report_file, '00index.html')
+    {'Name'=>@comparison,
+     'Static Report [Link]'=>report_link,
+     'Report [File]'=>report_file,
+    }
+  end
+  def commands
+    command = "module load #{@params["Rversion"]}\n"
+    command << run_RApp("EzAppSeuratCompare")
+  end
+end
+
+if __FILE__ == $0
+
+end