def upload_tenx(sampleid, before, finished):
print("Calling upload.")
tenx = TenxAnalysis("./{}/outs/".format(sampleid))
tenx.finalize()
tenxds = TenxDataStorage(sampleid)
tenxds.upload_cellranger(tenx)
open(finished, "w").write("Completed")
def Run(sampleid, finished):
if not os.path.exists("cellranger.complete"):
CellRanger.count([sampleid])
tenx = TenxAnalysis("./{}/outs/".format(sampleid))
tenx.finalize()
tenxds = TenxDataStorage(sampleid)
tenxds.upload_cellranger(tenx)
open(finished,"w").write("Completed")
def RunUpload(sampleid, finished, species):
print("Uploading ",species, sampleid)
tenx_output = os.path.join(config.jobpath,"{}/outs/".format(sampleid))
tenx = TenxAnalysis(tenx_output)
tenx.finalize()
tenxds = TenxDataStorage(sampleid, species=species)
print("Running upload")
tenxds.upload_cellranger(tenx)
open(finished,"w").write("Completed")
def upload(self, tenx):
outs = self.get_output()
tenx = TenxAnalysis(outs)
tenx.finalize()
storage = DataStorage(self.prefix)
storage.upload_results(tenx)
