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check: Adding line number to error messages. #392

Merged
merged 1 commit into from
Jul 3, 2024
Merged

check: Adding line number to error messages. #392

merged 1 commit into from
Jul 3, 2024

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smoe
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@smoe smoe commented Jul 1, 2024

Hello,

ported this to dev but was running master when I got an error message that was triggered by an empty last line in the sample sheet. Found that only after adding line numbers to the error message and thought that this may be of interest to everyone to have. So, here it comes.

The change are the addition of an iterator and the formatting of the error message's context from "Line" to "Line {}".format(lineNo). For the error message on an invalid number of columns I also added the actual number of columns that were found.

Best,
Steffen

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    Would be happy to do so but need a bit of an instruction on how you want to integrate that into the testing on samplesheets that is already performed.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
    Tested the script on a local file.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).
    Not required.

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github-actions bot commented Jul 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 80a12ac

+| ✅ 227 tests passed       |+
#| ❔   2 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-07-03 14:05:48

JoseEspinosa
JoseEspinosa requested changes Jul 3, 2024
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Thanks for contributing @smoe! 😄
Would be nice if you could address my suggestions 🙏

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@smoe
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smoe commented Jul 3, 2024

Thanks for contributing @smoe! 😄 Would be nice if you could address my suggestions 🙏

All accepted, very nice, many thanks! Let me quickly rebase this to reduce the number of commits. I presume you are happy with me squashing this all into one.

JoseEspinosa
JoseEspinosa approved these changes Jul 3, 2024
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Thanks @smoe!
LGTM! 🚀

@smoe @JoseEspinosa
check: Adding line number to error messages.
80a12ac 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
@smoe smoe force-pushed the adding_line_numbers_to_check_dev branch from 848b9f1 to 80a12ac Compare July 3, 2024 13:42
@JoseEspinosa JoseEspinosa merged commit c3e1861 into nf-core:dev Jul 3, 2024
9 checks passed
@smoe smoe deleted the adding_line_numbers_to_check_dev branch July 3, 2024 15:11
@JoseEspinosa JoseEspinosa mentioned this pull request Jul 3, 2024
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@smoe @JoseEspinosa