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Diffstat (limited to 'workflows/pangenome-generate/collect-seqs.py')
| -rw-r--r-- | workflows/pangenome-generate/collect-seqs.py | 2 |
1 files changed, 2 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py index cb5bc33..9a89549 100644 --- a/workflows/pangenome-generate/collect-seqs.py +++ b/workflows/pangenome-generate/collect-seqs.py @@ -3,6 +3,7 @@ import arvados import json import shutil import logging +import subprocess import arvados.collection import ruamel.yaml import schema_salad.schema @@ -71,5 +72,6 @@ for item in validated: except Exception as e: logging.exception("Error processing collection %s" % uuid) +subprocess.run(["samtools", "faidx", "relabeledSeqs.fasta"]) shutil.rmtree(".cache") |