orequired.append(Parameter("project_id","The project id the run belongs to","--project-id",required=True,type=int,group="Run information"))
orequired.append(Parameter("project_id","The project id the run belongs to","--project-id",required=True,type=existingproject,group="Run information"))
orequired.append(Parameter("run_name","Give a name to your run","--name",required=True,group="Run information",display_name="Name"))
orequired.append(Parameter("run_description","Give a description to your run","--description",required=True,group="Run information",display_name="Description"))
orequired.append(Parameter("run_date","When were the data produced","--date",required=True,type=date,group="Run information",display_name="Date"))
...
...
@@ -145,51 +142,62 @@ class NG6Workflow (BasicNG6Workflow):
def_add_sample_parameters(self):
osamples=[]
subparams=[]
subparams.append(Parameter("sample_name","The name of the sample, MID for 454 data","sample_name"))
subparams.append(Parameter("sample_id","The uniq identifier of the sample","sample_id"))
subparams.append(Parameter("sample_name","A descriptive name for the sample","sample_name"))
subparams.append(Parameter("sample_description","A brief description of the sample","sample_description"))
subparams.append(Parameter("read1","Read 1 data file path","read1",required=True,type="localfile",action="append"))
subparams.append(Parameter("read2","Read 2 data file path","read2",type="localfile",action="append"))
subparams.append(Parameter("type","Read orientation and type","type",choices='|'.join(Sample.AVAILABLE_TYPES)))
subparams.append(Parameter("insert_size","Insert size for paired end reads","insert_size",type='int'))
subparams.append(Parameter("species","Species related to this sample","species"))
subparams.append(Parameter("nb_sequence","Number of sequences in the sample file","nb_sequence",type='int'))
osamples.append(Parameter("sample","Definition of a sample","--sample",action="append",type="multiple",required=True,sub_parameters=subparams,group="exclude-sample"))
@@ -243,23 +250,11 @@ class CasavaNG6Workflow(NG6Workflow):
params.append(Parameter("casava","Definition of a casava directory for sample retrieving","--casava",required=True,sub_parameters=subparams,type="multiple",group="exclude-sample"))
assertlen(barcodes_list)==len(sample_ids_list)==len(subdirs_list),"Invalid lane {0} for project {1} in SampleSheet.mk".format(lane_number,project_name)