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nf-validation on sample sheet #87

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2 tasks done
Daniel-VM opened this issue Sep 20, 2023 · 3 comments
Closed
2 tasks done

nf-validation on sample sheet #87

Daniel-VM opened this issue Sep 20, 2023 · 3 comments
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enhancement New feature or request

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@Daniel-VM
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Daniel-VM commented Sep 20, 2023

Sample sheet validation could be performed via nf-validation plugin.
In addition, tsv/csv documentation and parsing will need adjustments.

  • Fix README: tsv file extension on sample sheet will fail, change it to csv
    - [ ] Update test data-set (nf-core/test-dataset::bacass ). Two options:
    - Switch from tab to comma separated content/structure on sample sheets for testing (I prefer this one) .
    - Or Change file extensions on sample sheets from csv to tsv
  • Add nf-validation on sample sheet
@Daniel-VM Daniel-VM added the enhancement New feature or request label Sep 20, 2023
@Daniel-VM Daniel-VM self-assigned this Sep 20, 2023
@Daniel-VM
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Validation fails on the sample sheet when attempting to read a tab-separated file with a *.csv extension.

This issue affects all test datasets within nf-core/test-dataset::bacass. It might be advisable to consider changing the file extension from csv to tsv for the test dataset files.

@d4straub
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d4straub commented Sep 21, 2023

We could just add the same files with a tsv ending. I think its better to leave the old files in to keep older bacass versions with -profile test running. Do you want to do it or should I?

@Daniel-VM
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Daniel-VM commented Sep 21, 2023

Yes!. I agree. I'll do it ;).

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