Commit effc7180 by MARIJON Pierre

we didn't need merge file

parent a2cce4e7
......@@ -107,27 +107,27 @@ def finish(args):
logging.info("end finish canu assembly")
#merge file
logging.info("begin merge fastq for mini{map|asm}")
cat_call = "cat {}".format(" ".join(fastq_files))
merged_fastq = str(data_path / "merged.fastq")
merged_fastq_log = merged_fastq + ".log"
# logging.info("begin merge fastq for mini{map|asm}")
# cat_call = "cat {}".format(" ".join(fastq_files))
# merged_fastq = str(data_path / "merged.fastq")
# merged_fastq_log = merged_fastq + ".log"
logging.info(cat_call)
# logging.info(cat_call)
with open(merged_fastq_log, "w") as errfile:
with open(merged_fastq, "w") as outfile:
pass
out = subprocess.call(cat_call.split(" "),
stdout=outfile,
stderr=errfile,
universal_newlines=True)
logging.info("end merge fastq for mini{map|asm}")
# with open(merged_fastq_log, "w") as errfile:
# with open(merged_fastq, "w") as outfile:
# pass
# out = subprocess.call(cat_call.split(" "),
# stdout=outfile,
# stderr=errfile,
# universal_newlines=True)
# logging.info("end merge fastq for mini{map|asm}")
minimap_path = args["assembly"] / accession / "minimap"
minimap_path.mkdir(parents=True, exist_ok=True)
logging.info("begin minimap")
minimap_call = minimap_call_template.format(merged_fastq, merged_fastq)
minimap_call = minimap_call_template.format(fastq_files, fastq_files)
minimap_out = str(minimap_path / "minimap.paf")
minimap_log = str(minimap_path / "minimap.log")
......
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