Commit 926392ab authored by ckuchly's avatar ckuchly
Browse files

#139 clean code

parent 7b313894
...@@ -190,9 +190,6 @@ class NG6Workflow (BasicNG6Workflow): ...@@ -190,9 +190,6 @@ class NG6Workflow (BasicNG6Workflow):
pidx = 1 pidx = 1
nidx = 1 nidx = 1
for rang, sample in enumerate(self.samples) : for rang, sample in enumerate(self.samples) :
print(sample)
print("sample readsi")
print(sample.readsi)
if sample.name : if sample.name :
self.samples_names.append(sample.name) self.samples_names.append(sample.name)
else : else :
...@@ -686,8 +683,7 @@ class CasavaNG6Workflow(NG6Workflow): ...@@ -686,8 +683,7 @@ class CasavaNG6Workflow(NG6Workflow):
# archive the files # archive the files
#TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory() #TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
logging.getLogger("CasavaNG6Workflow").debug("illumina_process filter reads = " + ",".join(filtered_read1_files))
logging.getLogger("CasavaNG6Workflow").debug("illumina_process readsi =" + ",".join(self.get_all_reads("index")))
saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index") saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index")
logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files)) logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
reads_prefixes = None reads_prefixes = None
...@@ -695,7 +691,7 @@ class CasavaNG6Workflow(NG6Workflow): ...@@ -695,7 +691,7 @@ class CasavaNG6Workflow(NG6Workflow):
# concatenate fastq # concatenate fastq
reads_prefixes = list((Utils.get_group_basenames(saved_files, "read")).keys()) reads_prefixes = list((Utils.get_group_basenames(saved_files, "read")).keys())
logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files)) logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files, reads_prefixes]) concatenatefastq = self.add_component("ConcatenateFilesGroups", [self.runobj,saved_files,reads_prefixes])
saved_files = concatenatefastq.concat_files saved_files = concatenatefastq.concat_files
logging.getLogger("CasavaNG6Workflow").debug("illumina_process after concatenatefastq, saved_files = " + ",".join(saved_files)) logging.getLogger("CasavaNG6Workflow").debug("illumina_process after concatenatefastq, saved_files = " + ",".join(saved_files))
......
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