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authorPeter Amstutz2020-07-07 15:52:46 -0400
committerPeter Amstutz2020-07-07 15:55:06 -0400
commit7cf561c1b92a44d488d36dd3d883750b261c6550 (patch)
treebdcc34b45f0dd31dfcb15d44c4049ec9ea46b51f /bh20sequploader/main.py
parent4f30e506055acb788a1ff1bbcb6359c4413a4eab (diff)
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Use minimap2 instead of clustalw for fasta QC
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20sequploader/main.py')
-rw-r--r--bh20sequploader/main.py9
1 files changed, 7 insertions, 2 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8555e2b..fd0278d 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -23,14 +23,16 @@ ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
+ failed = False
try:
log.debug("Checking metadata" if do_qc else "Skipping metadata check")
if do_qc and not qc_metadata(metadata.name):
- raise Exception("Failed metadata qc")
+ log.warning("Failed metadata qc")
+ failed = True
except Exception as e:
log.debug(e)
print(e)
- exit(1)
+ failed = True
target = []
try:
@@ -43,6 +45,9 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
except Exception as e:
log.debug(e)
print(e)
+ failed = True
+
+ if failed:
exit(1)
return target