8000 Add new classifer: ganon by jfy133 · Pull Request #298 · nf-core/taxprofiler · GitHub
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Add new classifer: ganon #298

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Merged
merged 15 commits into from
Jun 29, 2023
Merged

Add new classifer: ganon #298

merged 15 commits into from
Jun 29, 2023

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@jfy133 jfy133 commented May 26, 2023 •
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Started added ganon - not yet complete -> firstly the test isn't working as ganon isn't picking up any hits (updatE: this was because it didn't like long read data), and I have not yet completed the entire workflow (see hackmd)

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/taxprofiler 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).

@jfy133 jfy133 added the WIP Work in progress label May 26, 2023
@jfy133 jfy133 self-assigned this May 26, 2023
@jfy133 jfy133 marked this pull request as draft May 26, 2023 18:32
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github-actions bot commented May 26, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3269e31

+| ✅ 158 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • schema_lint - Schema 'description' should be 'Taxonomic classification and profiling of shotgun and long-read metagenomic data'
    Found: 'Taxonomic classification and profiling of shotgun metagenomic data'

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-29 15:15:19

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jfy133 commented May 28, 2023 •
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TODO:

  • Add merge table subcommand in standardisation_profiles
  • Update docs and workflow diagram
    • README
    • Citations.md
    • Workflow diagram
    • Schema
    • Usage
    • Output
  • Update module to export log (for MultiQC purposes)
  • Write MultiQC module
  • Write taxpasta module
  • Make fulltest database

@jfy133 jfy133 marked this pull request as ready for review June 12, 2023 10:27
@jfy133 jfy133 requested a review from a team June 12, 2023 10:27
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jfy133 commented Jun 12, 2023

Conceptually this now works except for the MultiQC/taxpasta stuff, which we can update in the future anyway!

Update flow: https://hackmd.io/@jfy133/rJ3rM6hHn

@jfy133 jfy133 linked an issue Jun 23, 2023 that may be closed by this pull request
New classifier: GANON #246
Closed
@jfy133 jfy133 removed the WIP Work in progress label Jun 25, 2023
sofstam
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Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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One formatting thing and I think it can be ready to go!

jfy133
jfy133 commented Jun 29, 2023
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jfy133 commented Jun 29, 2023

I added "kmcp" to the list of allowed databases in the database calidatio ncheck now that it's in the database sheet in test-datasets 😬

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sofstam commented Jun 29, 2023 •
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@jfy133 The changelog should be updated as well :)

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jfy133 commented Jun 29, 2023

@sofstam updated changelog and put back the right database sheet for KrakenUniq!

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sofstam commented Jun 29, 2023

I think you can merge now :)

@jfy133 jfy133 changed the title Start adding ganon Add new classifer: ganon Jun 29, 2023
@jfy133 jfy133 merged commit 7409c20 into dev Jun 29, 2023
@jfy133 jfy133 deleted the new-profiler-ganon branch June 29, 2023 17:27
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New classifier: GANON
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