diff options
Diffstat (limited to 'bh20seqanalyzer')
| -rw-r--r-- | bh20seqanalyzer/main.py | 9 |
1 files changed, 8 insertions, 1 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 1fb51b5..c05b402 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -8,6 +8,7 @@ import json import logging import ruamel.yaml from bh20sequploader.qc_metadata import qc_metadata +from bh20sequploader.qc_fasta import qc_fasta import pkg_resources from schema_salad.sourceline import add_lc_filename @@ -38,7 +39,13 @@ def validate_upload(api, collection, validated_project, logging.warn("Failed metadata qc") if valid: - if "sequence.fasta" not in col: + if "sequence.fasta" in col: + try: + qc_fasta(col.open("sequence.fasta")) + except Exception as e: + logging.warn(e) + valid = False + else: if "reads.fastq" in col: start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid) return False |