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Custom gmt (11)#172

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WackerO merged 22 commits intoqbic-pipelines:devfrom
WackerO:custom_gmt
Dec 13, 2022
Merged

Custom gmt (11)#172
WackerO merged 22 commits intoqbic-pipelines:devfrom
WackerO:custom_gmt

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@WackerO WackerO commented Nov 24, 2022

This PR adds the possibility of providing a custom GMT file for the pathway analysis which will be used instead of doing an online query on gprofiler. Alternatively, when doing the online query, the pipeline will now attempt to download the corresponding GMT file. Closes #72

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/rnadeseq 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).

@WackerO WackerO marked this pull request as draft November 24, 2022 10:39
@WackerO WackerO marked this pull request as ready for review December 5, 2022 07:54
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@ggabernet ggabernet left a comment

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Looks good to me, but please also add documentation about this in the usage.md docs.

Comment thread assets/RNAseq_report.Rmd Outdated
WackerO and others added 2 commits December 13, 2022 15:47
Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com>
@WackerO WackerO merged commit a4eade0 into qbic-pipelines:dev Dec 13, 2022
@WackerO WackerO deleted the custom_gmt branch December 13, 2022 14:56
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2 participants