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Decompress stream#223

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joverlee521 wants to merge 8 commits intomasternextstrain/ncov-ingest:masterfrom decompress-streamnextstrain/ncov-ingest:decompress-streamCopy head branch name to clipboard

+42-32

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Commits on Oct 18, 2021

• fetch-from-gisaid: compress download with xz

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  b063d38

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• notify-on-record-change: support .xz source file

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Commits on Oct 26, 2021

• upload-to-s3: skip compression if src is compressed

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  2be0387

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• download-from-s3: skip decompression if dst is compressed

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• transform-gisaid: remove trailing whitespace

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• transform-gisaid: use lzma to read .xz file

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• ingest-gisaid: use gisaid.ndjson.xz file

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• run-nextclade-full: keep input FASTA compressed

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