closes #14 execute pipeline from a single config on cluster

pipeline_start_template.yaml

@@ -1,8 +1,7 @@
 project_Name: test
 mapping:
- fastQ_directory_path: /test/
+ fastQ_directory_path: /home/immanuel/Documents/test_project/test_data
  proc: 16
  aligner: tophat2
  genome: mouse
- strand: 
-
+ strand: 

src/analysis_framework.py

@@ -93,9 +93,8 @@ def writeMappingScript(self,userInput): #writes mapping script
 			outdir = inputs.projName()+"/"+line+"."+ inputs.aligner()
 			align = Mapping(self.fastqs.read1(sample),inputs.proc(), outdir,settings.genomes()[inputs.genome()][inputs.aligner()],fastqR2=self.fastqs.read2(sample))
 
-
-			if inputs.aligner() == "tophat2":
-				if settings.getEnv()["cluster"] is not 'None':
+			if inputs.aligner() == "tophat2": #logic for tophat alignment...
+				if settings.getEnv()["cluster"] is not 'None': #...on a cluster such as minerva
 					file = open(settings.homeDir()+"/"+inputs.projName()+"/"+"scripts/mapping/"+line+".tophat2.mapping.pbs", "w") #change to relative path
 					#insert pbs headers
 					#insert load modules

src/complete_seq.py

@@ -16,17 +16,9 @@ def main():
 	directories  = SetProjectEnv(settings.homeDir(),pipeline_command.projName())
 	writer = ScriptWriter() #simplify this
 
-
 	directories.makeProj() #project directory created
 	directories.startMappingEnv() #mapping subdirectories created
 	writer.writeMappingScript(options.pipeline_input)
-	# make project environment
-
-	# write project scripts
-	# launch project scripts
-
-
-
 
 if __name__ == '__main__':
     main()