Support vanilla GISAID downloads #701
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I just noticed 2abdf4d is redundant with @jameshadfield's PR #691, so we should merge that PR first and then I'll rebase this onto that without the first commit. |
Uses GISAID's new convention of replacing whitespace with underscores in strain names so metadata and sequence data match when using search downloads.
To support GISAID's patient status metadata as an input format that's consistent with the rest of our workflow, map the "Lineage" column to its Nextstrain equivalent (since this column contains the PANGO lineage).
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Documents two options for downloading search results including the original "Augur" download and the two separate GISAID downloads that have always been available.
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The ncov PR 701 [1] expanded the ncov tutorial to include a description of how to download search results from GISAID as two separate files. This commit adds the corresponding screenshots for that documentation. [1] nextstrain/ncov#701
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Description of proposed changes
Support a workflow that includes inputs from the GISAID Search interface including "Sequences (FASTA)" (converting spaces to underscores) and "Patient status metadata" (both shown below)
These files technically contain the information we need to run the workflow, given the minor changes in this PR.
Testing
Release checklist
If this pull request introduces new features, complete the following steps:
docs/change_log.mdin this pull request to document these changes by the date they were added.