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| author | Peter Amstutz | 2020-11-18 17:03:01 -0500 |
|---|---|---|
| committer | Peter Amstutz | 2020-11-18 17:05:12 -0500 |
| commit | 81daa0acc4c4a0827e1c1198f054f4d4dacd1daf (patch) | |
| tree | b1370c876394e36cb65947dbb37b094536d117ed /workflows/pangenome-generate/collect-seqs.py | |
| parent | ee8ea88dd6b372143c6b08f56856666ce2d0b622 (diff) | |
| download | bh20-seq-resource-81daa0acc4c4a0827e1c1198f054f4d4dacd1daf.tar.gz bh20-seq-resource-81daa0acc4c4a0827e1c1198f054f4d4dacd1daf.tar.lz bh20-seq-resource-81daa0acc4c4a0827e1c1198f054f4d4dacd1daf.zip | |
Add query-to-gfa workflow
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
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") |