Commit ac60fda7 authored by maxime mano's avatar maxime mano
Browse files

add param barcode file and barcode score

parent 19e57461
......@@ -172,7 +172,10 @@ class RS_Subreads (Analysis):
self.name = "RS_Subreads"
self.description = "Run SMRTAnalysis RS_Subreads.1"
self.software = "Python"
self.options = "minSubReadLength %s readScore %s minLength %s"%(self.min_subreads_length, self.polymerase_read_qual, self.polymerase_read_length)
if self.barcode_file :
self.options = "minSubReadLength %s readScore %s minLength %s Barcode file %s Barcode score %s"%(self.min_subreads_length, self.polymerase_read_qual, self.polymerase_read_length, self.barcode_file, self.barcode_score)
else :
self.options = "minSubReadLength %s readScore %s minLength %s"%(self.min_subreads_length, self.polymerase_read_qual, self.polymerase_read_length)
def post_process(self):
logging.getLogger("jflow").debug("Begin RS_Subreads.post_process!")
......@@ -272,7 +275,7 @@ class RS_Subreads (Analysis):
demultiplex_fasta_tar = os.path.join(sample_outdir,'data','barcoded-fastqs.tgz')
logging.getLogger("jflow").debug("demultiplex_fasta_tar : " + demultiplex_fasta_tar)
results_files.append(demultiplex_fasta_tar)
self._create_and_archive(results_files,"Archive_Barcode")
if group not in metrics2 :
......
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