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authorPeter Amstutz2020-11-09 17:20:27 -0500
committerPeter Amstutz2020-11-09 17:20:27 -0500
commit1082b907d816f5da52aba6233073737632d0242f (patch)
tree8ad59d268234bbea42b3d6b42bd2d352eb56df28 /workflows/pangenome-generate
parentb5143c79de268b844f3a6a63d92c6389b047f35e (diff)
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Make resource link work for both portable data hashes and sample id
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate')
-rw-r--r--workflows/pangenome-generate/collect-seqs.py2
1 files changed, 1 insertions, 1 deletions
diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py
index af4a0dc..1a0807c 100644
--- a/workflows/pangenome-generate/collect-seqs.py
+++ b/workflows/pangenome-generate/collect-seqs.py
@@ -38,7 +38,7 @@ for item in validated:
pdh = item["portable_data_hash"]
with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col:
with col.open("sequence.fasta", "rt") as fa:
- subject = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % pdh
+ subject = "http://covid19.genenetwork.org/resource/%s" % pdh
label = fa.readline().strip()
merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subject, label[1:].replace('"', '\\"')))
skip = (subject in blacklist or label[1:] in blacklist)