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Add support to handle (tdf) archives #323

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merged 13 commits into from
May 29, 2024

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jonasscheid
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@jonasscheid jonasscheid commented May 14, 2024

This PR introduces a new subworkflow prepare_spectra, which takes care of all steps related to file conversion to mzml and centroiding pre-search.

New modules:

  • UNTAR
  • UNZIP
  • GUNZIP

Now the following file extentions are supported and handeled properly:

d|d.tar.gz|d.tar|d.zip|mzML.gz|raw|RAW|mzML

This implementation allows to test immunopeptidomics bruker files and allows to process Bruker files straight from PRIDE🥳

  • 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).

@jonasscheid jonasscheid changed the base branch from master to dev May 14, 2024 12:02
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github-actions bot commented May 14, 2024

nf-core lint overall result: Passed ✅

Posted for pipeline commit 528e77f

+| ✅ 236 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-28 20:58:14

@nf-core nf-core deleted a comment from github-actions bot May 14, 2024
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@marissaDubbelaar marissaDubbelaar left a comment

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LGTM

@jonasscheid jonasscheid merged commit 0fd0045 into nf-core:dev May 29, 2024
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@jonasscheid jonasscheid mentioned this pull request May 30, 2024
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This was referenced Jun 17, 2024
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2 participants