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this updates the nextalign and nextclade calls to work with nextclade v2.

will require nextclade v2 in the image.

The trial build completed without problem!

--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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