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Alter the tsv outcome of quantified data #292

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Alter the tsv outcome of quantified data #292

wants to merge 6 commits into from

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marissaDubbelaar
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Fix for #291
Here, an R script is included to make the TSV data readable.

  • columns that have an ID that corresponds with HUPO Proteomics Standards are renamed to their definition.
  • Sequences without mutation information are included
  • Mutation information is additionally included in another column
  • Peptide and consensus information is transformed into a readable format

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 Nov 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 93ea7db

+| ✅ 156 tests passed       |+
!| ❗   8 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.5.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in WorkflowMhcquant.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 51]
  • 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]

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-01 12:14:42

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@marissaDubbelaar