8000 GUNC output overwriting itself · Issue #502 · nf-core/mag · GitHub
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GUNC output overwriting itself #502

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maxibor opened this issue Sep 1, 2023 · 1 comment
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GUNC output overwriting itself #502

maxibor opened this issue Sep 1, 2023 · 1 comment
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@maxibor
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maxibor commented Sep 1, 2023

Description of the bug

Gunc outputs are being overwritten is the result directory: the output file name of gunc is GUNC.{DB version}maxCSS_level.tsv and {PREFIX}.all_levels.tsv. (see GUNC doc)

Because GUNC is run per bin in nf-core/mag, but the results are saved per [assembler]-[binner]-[sample] (See code here) (and should probably be [assembler]-[binner]-[domain]-[refinement]-[sample] according to #489 ) and are therefore being overwritten.

Note that the gunc summary is not affected, and the gunc_summary.tsv file is fine.

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@maxibor maxibor added the bug Something isn't working label Sep 1, 2023
@jfy133
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jfy133 commented Sep 2, 2023 •
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Personal i.e., once #489, have a second PR to update the prefix.

Note we should also possible update prefix for PROKKA which may also have the same problem., which as far as I can see is the only other module that should be affected that is downstream of binninng

@adamrtalbot adamrtalbot mentioned this issue Sep 7, 2023
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@jfy133 jfy133 mentioned this issue Sep 26, 2023
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@jfy133 jfy133 closed this as completed Oct 3, 2023
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