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| author | Peter Amstutz | 2020-07-03 21:15:48 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-03 21:15:48 +0000 |
| commit | 38340e0cedb465cd592ac40b11c9d22c75973fed (patch) | |
| tree | 92e9834c68edcb93a6597d091b337318675af33d /bh20sequploader/main.py | |
| parent | 04df498f5cd85015afce79e1e87a3979e596dcc6 (diff) | |
| download | bh20-seq-resource-38340e0cedb465cd592ac40b11c9d22c75973fed.tar.gz bh20-seq-resource-38340e0cedb465cd592ac40b11c9d22c75973fed.tar.lz bh20-seq-resource-38340e0cedb465cd592ac40b11c9d22c75973fed.zip | |
Add --skip-qc for faster batch import
Diffstat (limited to 'bh20sequploader/main.py')
| -rw-r--r-- | bh20sequploader/main.py | 4 |
1 files changed, 2 insertions, 2 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index dc63bfc..cdc4c3f 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -24,7 +24,7 @@ UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): try: - log.debug("Checking metadata") + log.debug("Checking metadata" if do_qc else "Skipping metadata check") if do_qc and not qc_metadata(metadata.name): log.warning("Failed metadata qc") exit(1) @@ -36,7 +36,7 @@ def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): target = [] try: - log.debug("Checking FASTA/FASTQ QC") + log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC") target.append(qc_fasta(sequence_p1, check_with_clustalw=do_qc)) if sequence_p2: target.append(qc_fasta(sequence_p2)) |