From ce3030d983557bcc5149d330bfd0c1ca7b8c05b2 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 10 Sep 2024 11:37:00 -0700 Subject: [PATCH 1/2] Fix whitespace --- nextclade/Snakefile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nextclade/Snakefile b/nextclade/Snakefile index 56d824d..f9800ec 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/ """ - From 2e8211dd1b03b57ba92b835826d6a5e18a57cf27 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 10 Sep 2024 14:17:15 -0700 Subject: [PATCH 2/2] Rename metadata column from `isolate_id` to `gisaid_epi_isl` MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The fields to export in acknowledgements is hardcoded in Auspice¹ so the metadata field needs to be named `gisaid_epi_isl` to be included in the acknowledgements for the seasonal flu builds. Renaming the column in our upload config to avoid having to rename it as part of the phylogenetic workflow. ¹ --- profiles/upload.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/profiles/upload.yaml b/profiles/upload.yaml index 50f09e0..602a354 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