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Switch to and to so that the abbreviated author field is used by in t…
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…he phylogenetic workflow.
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DOH-LMT2303 committed Jan 13, 2025
1 parent 42e5062 commit 1863ab3
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions ingest/defaults/config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ curate:
isolate-lineage-source: sample_type
biosample-acc: biosample_accessions
sra-accs: sra_accessions
submitter-names: authors
submitter-names: full_authors
submitter-affiliation: institution
# Standardized strain name regex
# Currently accepts any characters because we do not have a clear standard for strain names across pathogens
Expand All @@ -83,11 +83,11 @@ 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"
Expand Down Expand Up @@ -117,7 +117,7 @@ curate:
'is_lab_host',
#'date_submitted',
#'sra_accession',
#'abbr_authors',
#'full_authors',
#'reverse',
'authors',
'latitude',
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