Merge pull request #179 from nextstrain/upload-gisaid-epi-isl

Rename metadata column from `isolate_id` to `gisaid_epi_isl`
nextstrain · Oct 10, 2024 · b0ff43d · b0ff43d
2 parents c696e8a + 2e8211d
commit b0ff43d
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diff --git a/nextclade/Snakefile b/nextclade/Snakefile
@@ -415,7 +415,7 @@ rule export:
         date=datetime.datetime.utcnow().strftime("%Y-%m-%d"),
     shell:
         """
-        tsv-select -H -f {params.select_fields} {input.metadata} > {input.metadata}.tmp 
+        tsv-select -H -f {params.select_fields} {input.metadata} > {input.metadata}.tmp
         augur export v2 \
             --tree {input.tree} \
             --metadata {input.metadata}.tmp \
@@ -494,4 +494,3 @@ rule clean_all:
         rm -rf datasets
         rm -rf data/
         """
-
diff --git a/profiles/upload.yaml b/profiles/upload.yaml
@@ -25,7 +25,7 @@ fasta_fields:
   - strain
   - virus
   - segment
-  - isolate_id
+  - gisaid_epi_isl
   - accession
   - date
   - date_submitted