From ba9442943753e0bb9ce5014f9dd264238b15f614 Mon Sep 17 00:00:00 2001 From: Jover Lee Date: Tue, 19 Nov 2024 15:22:46 -0800 Subject: [PATCH] ingest: Switch to `full_authors` and `authors` fields Switch `authors` to `full_authors` and `abbr_authors` to `authors` so that the abbreviated author field is used by `augur export` in the phylogenetic workflow. --- ingest/defaults/config.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ingest/defaults/config.yaml b/ingest/defaults/config.yaml index 7bd0362..83f992d 100644 --- a/ingest/defaults/config.yaml +++ b/ingest/defaults/config.yaml @@ -61,7 +61,7 @@ curate: is-lab-host: is_lab_host isolate-lineage-source: sample_type biosample-acc: biosample_accessions - submitter-names: authors + submitter-names: full_authors submitter-affiliation: institution submitter-country: submitter_country # Standardized strain name regex @@ -88,11 +88,11 @@ curate: "los", "nad", "of", "op", "sur", "the", "y" ] # Metadata field that contains the list of authors associated with the sequence - authors_field: "authors" + authors_field: "full_authors" # Default value to use if the authors field is empty authors_default_value: "?" # Name to use for the generated abbreviated authors field - abbr_authors_field: "abbr_authors" + abbr_authors_field: "authors" # Path to the manual annotations file # The path should be relative to the ingest directory annotations: "defaults/annotations.tsv" @@ -119,6 +119,6 @@ curate: "date_updated", "sra_accessions", "authors", - "abbr_authors", + "full_authors", "institution", ]