Feat/upgrade nextclade #963
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I started a trial build using the v2 docker image. results should show up here: https://nextstrain.org/staging/ncov/open/trial/nextclade-v2/REGION_NAME |
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The trial build completed without problem! |
fanninpm
reviewed
Jun 22, 2022
| --sequences /dev/stdin \ | ||
| --output-dir {params.outdir} \ | ||
| --output-basename {params.basename} \ | ||
| --output-translations {params.output_translations} \ | ||
| --output-fasta {params.uncompressed_alignment} \ |
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According to the changelog, version 2 of the Nextalign CLI can write compressed output files, perhaps rendering the uncompressed_alignment parameter unnecessary.
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this updates the nextalign and nextclade calls to work with nextclade v2.
will require nextclade v2 in the image.