diff --git a/nextclade/Snakefile b/nextclade/Snakefile index 56d824d8..f9800ec4 100644 --- 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 index 50f09e0a..602a354d 100644 --- 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