Commit 7b313894 authored by ckuchly's avatar ckuchly

debug : saved.files add all reads or we want just filtered files.

parent 5687a776
......@@ -686,13 +686,14 @@ 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")
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")
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])
saved_files = concatenatefastq.concat_files
......
Markdown is supported
0%
or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment