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feat: support sample-specific genome assembly & version params #70

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uniqueg opened this issue Sep 6, 2023 · 0 comments
Open

feat: support sample-specific genome assembly & version params #70

uniqueg opened this issue Sep 6, 2023 · 0 comments
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future will not be fixed for NOW

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@uniqueg
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uniqueg commented Sep 6, 2023

Problem

Currently, it is not possible to specify genome assemblies and corresponding versions on a per-sample basis, making it cumbersome to run samples originating from the same or from different sources against different genome assemblies or versions (the workaround is to specify the genome and gene annotation files directly).

Possible solution

Allow for additional optional fields genome_assembly and resource_version in the sample table. If provided, HTSinfer-based source inference is disabled and genomepy is triggered to fetch the specified version of the specified assembly (or the default assembly for the sample source/organism, if provided), if not already available.

@uniqueg uniqueg added the future will not be fixed for NOW label Sep 6, 2023
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