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| author | Peter Amstutz | 2020-07-07 15:52:46 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-07 15:55:06 -0400 |
| commit | 7cf561c1b92a44d488d36dd3d883750b261c6550 (patch) | |
| tree | bdcc34b45f0dd31dfcb15d44c4049ec9ea46b51f /bh20sequploader/main.py | |
| parent | 4f30e506055acb788a1ff1bbcb6359c4413a4eab (diff) | |
| download | bh20-seq-resource-7cf561c1b92a44d488d36dd3d883750b261c6550.tar.gz bh20-seq-resource-7cf561c1b92a44d488d36dd3d883750b261c6550.tar.lz bh20-seq-resource-7cf561c1b92a44d488d36dd3d883750b261c6550.zip | |
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.py | 9 |
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 |