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feat: write out samples table regardless of zarp being run or not #96

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ninsch3000 opened this issue Nov 3, 2024 · 0 comments
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@ninsch3000
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Is your feature request related to a problem? Please describe.
I'm not sure whether I just didn't find it, or whether it is not written, but in any case it would be nice to get an (incomplete) samples table as output from zarp-cli, even if zarp will not be invoked because of missing metadata. The incomplete table could then be filled in manually.
As I couldn't find the table, I had to copy htsinfer/results/samples_results.tsv, which does not contain paths to genome and annotation, or assemply version, etc.. Those latter values had been inferred after the htsinfer run through genomepy though.

Describe the solution you'd like
Regardless of whether zarp is invoked, or whether zarp-cli is run in PREPARE_RUN or RUN mode, write a samples.tsv with all the information that could be collected. Store this samples.tsv in an immediately obvious place.

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