Commit 16503d88 authored by Romain Therville's avatar Romain Therville 🐭

Merge branch '#139_debug' into 'master'

#139 debug

See merge request !63
parents 4b72adb5 926392ab
......@@ -190,9 +190,6 @@ class NG6Workflow (BasicNG6Workflow):
pidx = 1
nidx = 1
for rang, sample in enumerate(self.samples) :
print(sample)
print("sample readsi")
print(sample.readsi)
if sample.name :
self.samples_names.append(sample.name)
else :
......@@ -686,15 +683,15 @@ class CasavaNG6Workflow(NG6Workflow):
# archive the files
#TODO : if self.group_prefix == None, the create the output of fastqilluminafilter in the run.get_work_directory()
saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("readsi")
saved_files = filtered_read1_files + filtered_read2_files + self.get_all_reads("index")
logging.getLogger("CasavaNG6Workflow").debug("illumina_process saved_files = " + ",".join(saved_files))
reads_prefixes = None
if self.group_prefix != None :
# concatenate fastq
reads_prefixes = list((Utils.get_group_basenames(saved_files, "read")).keys())
logging.getLogger("CasavaNG6Workflow").debug("illumina_process reads_prefixes = " + ",".join(reads_prefixes))
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
logging.getLogger("CasavaNG6Workflow").debug("illumina_process after concatenatefastq, saved_files = " + ",".join(saved_files))
......
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