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mzml renaming and fixed ion parameters #301

Merged
merged 4 commits into from
Jan 6, 2024
Merged

mzml renaming and fixed ion parameters #301

merged 4 commits into from
Jan 6, 2024

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steffenlem
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@steffenlem steffenlem commented Jan 5, 2024 •
edited by jonasscheid
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Changes:

  1. The specification of other ions besides b/y did not work since those parameters required "--" instead of "-" for comet adapter.
  2. I changed the renaming of mzml files after the filter filtering step. Only when specifying the filtering step the mzml were renamed. This also affected the file names in all other places (e.g. ion annotations)

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/mhcquant 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>).
  • 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).

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github-actions bot commented Jan 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aea21d6

+| ✅ 162 tests passed       |+
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowMhcquant.groovy: Optionally add in-text citation tools to this list.
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 18]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 45]
  • system_exit - System.exit in WorkflowMhcquant.groovy: System.exit(1) [line 51]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 51]

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-05 16:29:50

@jonasscheid jonasscheid merged commit dc6c130 into nf-core:dev Jan 6, 2024
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@jonasscheid jonasscheid jonasscheid approved these changes

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@steffenlem @jonasscheid