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when file not found in DEEPCELL_MESMER test, the test is not run, so the issue isn't reported#76

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RobJY wants to merge 1 commit intonf-core:devfrom
RobJY:bugfix_DEEPCELL_MESMER_test
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when file not found in DEEPCELL_MESMER test, the test is not run, so the issue isn't reported#76
RobJY wants to merge 1 commit intonf-core:devfrom
RobJY:bugfix_DEEPCELL_MESMER_test

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@RobJY RobJY commented Jan 21, 2025

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).

I've changed to the tonsil file we usually use and new it's giving a new error, so looking into that as well.

So to be clear, there seem to be 2 issues.

  1. If the file is not found the test is not run.
  2. error generated from the file when found.

…we do not get an error; seeing if this changes that.
@RobJY RobJY self-assigned this Jan 21, 2025
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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RobJY commented Jan 21, 2025

Interestingly, removing checkIfExists: true from the call to file() allows the test suite to catch the error.

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