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Various fixes for the phylogenetic workflow automation #19
2 parents 10ff0af + 4b9e180 commit 86740e3

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ingest/build-configs/nextstrain-automation/upload.smk

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@@ -29,7 +29,7 @@ rule upload_to_s3:
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cloudfront_domain=config["cloudfront_domain"],
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shell:
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"""
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./scripts/upload-to-s3 \
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./vendored/upload-to-s3 \
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{params.quiet} \
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{input.file_to_upload:q} \
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{params.s3_dst:q}/{wildcards.remote_file:q} \

ingest/scripts/csv-to-ndjson

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ingest/scripts/fasta-to-ndjson

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ingest/scripts/fetch-from-genbank

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ingest/scripts/genbank-url

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ingest/scripts/join-metadata-and-clades.py

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ingest/scripts/ndjson-to-tsv-and-fasta

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