Ingest: Derive URL column during ingest #80
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ingest/rules/curate.smk
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| @@ -107,6 +107,8 @@ rule curate: | |||
| --abbr-authors-field {params.abbr_authors_field} \ | |||
| | augur curate apply-geolocation-rules \ | |||
| --geolocation-rules {input.all_geolocation_rules} \ | |||
| | jq -c --arg GENBANK "{params.id_field}" \ | |||
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If a workflow used strain as the id_field, this would create invalid URLs...Hmm, might be best to add a new config param (e.g. genbank_accession_field) that is explicitly for this command.
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Ah, good point, especially if we use id_field=strain for segmented viruses (e.g. flu or do you have an example? I assume in that case strain name is in the header line of sequences.fasta instead of genbank) to match isolates across tangle trees.
I can add an explicit genbank_accession_field here
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Thanks, added an explicit config['curate']['genbank_accession'] field during b2936f8
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After discussion: #76 (comment) Moved away from the |
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Description of proposed changes
Add URL column during ingest so the node call out works automatically. Attempting the
jqmethodRelated issue(s)
urlcolumn for accessions #76Checklist