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Correct nextflow schema entry for ref_data_hla_slice_bed #94

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scoughlan2
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This adds a missing type field, as outlined in issue #93, to an entry in the nextflow_schema.json

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!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/oncoanalyser branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core 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>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@scwatts scwatts self-requested a review September 6, 2024 22:29
@scwatts scwatts linked an issue Sep 6, 2024 that may be closed by this pull request
@scwatts scwatts added the enhancement New feature or request label Sep 6, 2024
@scwatts
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scwatts commented Sep 6, 2024

Hi @scoughlan2, thanks for the raising the issue and opening this PR to fix. Would you be able to rebase your above commit (4080193) on top of the nf-core:dev branch then force push to scoughlan2:master so that we don't duplicate the merge commit (4227bc1)?

I can sort that out if preferred!

@scoughlan2
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I have tried to rebase but cant quite get it to work so if you could sort it out, I would really appreciate it. Sorry for the extra work.

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scwatts commented Sep 9, 2024

Uh, that's weird. Looks like permissions for my user only allowed existing commits from the rebase to be pushed to your master branch, which excluded your commit and so automatically closed the PR then chain-closed the issue.

We should try this again using the standard approach with the dev branch rather than trying to fix and use the master branch. Could you please:

  • checkout the dev branch on your fork
  • make sure that it is up-to-date with nf-core remote (https://github.com/nf-core/oncoanalyser)
  • commit your change
  • open a new PR against the nf-core dev branch

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invalid file type: 'fastq'
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