Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Rename metadata column from isolate_id to gisaid_epi_isl #179

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Rename metadata column from isolate_id to gisaid_epi_isl #179

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ce3030d
Fix whitespace
joverlee521 Sep 10, 2024
2e8211d
Rename metadata column from `isolate_id` to `gisaid_epi_isl`
joverlee521 Sep 10, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 1 addition & 2 deletions nextclade/Snakefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 \
Expand Down Expand Up @@ -494,4 +494,3 @@ rule clean_all:
rm -rf datasets
rm -rf data/
"""

2 changes: 1 addition & 1 deletion profiles/upload.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ fasta_fields:
- strain
- virus
- segment
- isolate_id
- gisaid_epi_isl
- accession
- date
- date_submitted
Expand Down