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Disallow TXT files #304

Merged
merged 4 commits into from
Oct 24, 2024
Merged

Disallow TXT files #304

merged 4 commits into from
Oct 24, 2024

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WackerO
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@WackerO WackerO commented Oct 21, 2024

Currently, the pipeline does not properly handle contrast files with the TXT extension; they are treated as comma-separated which results in an error. This behaviour is now fixed.

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@WackerO WackerO requested a review from pinin4fjords October 21, 2024 12:33
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github-actions bot commented Oct 21, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d37e870

+| ✅ 299 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-23 06:55:05

pinin4fjords
pinin4fjords requested changes Oct 21, 2024
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@pinin4fjords pinin4fjords left a comment •
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I don't agree with this, you've just flipped the problem and created another one.

txt doesn't imply any particular separator- commas or tabs. Therefore we should just restrict the input to csv|tsv and disallow txt - not assume that txt has tabs.

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WackerO commented Oct 22, 2024

You're right, txt doesn't imply anything, but we have treated txt as a tab-separated file format for all the other files; your read_delim_flexible function makes the same assumption. I do think that we should treat this uniformly and either continue the same assumption here or disallow txt files in general.

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Yes, let's disallow!

@WackerO WackerO requested a review from pinin4fjords October 23, 2024 07:05
@WackerO WackerO changed the title Fix TXT contrast file bug Disallow TXT files Oct 23, 2024
@WackerO WackerO merged commit 3abee63 into nf-core:dev Oct 24, 2024
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@nschcolnicov nschcolnicov mentioned this pull request Nov 13, 2024
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@pinin4fjords pinin4fjords mentioned this pull request Nov 13, 2024
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@WackerO @pinin4fjords