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Add KrakenUniq Build #36

Merged
merged 9 commits into from
May 30, 2024
Merged

Add KrakenUniq Build #36

merged 9 commits into from
May 30, 2024

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jfy133
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@jfy133 jfy133 commented May 10, 2024

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/createtaxdb branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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 marked this pull request as draft May 10, 2024 11:11
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github-actions bot commented May 10, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e940613

+| ✅ 176 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-30 09:39:10

@jfy133 jfy133 marked this pull request as ready for review May 23, 2024 09:45
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jfy133 commented May 23, 2024 •
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OK this does work with conda, the KrakenUniq biocontainer is missing bc which is a dependency if you change the minimiser length.

@jfy133 jfy133 changed the title Start adding krakenuniq Add KrakenUniq Build May 30, 2024
@jfy133 jfy133 requested a review from sofstam May 30, 2024 09:01
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sofstam reviewed May 30, 2024
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🚀

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@jfy133 @sofstam
Update workflows/createtaxdb.nf
e940613 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
@sofstam sofstam requested review from sofstam and removed request for sofstam May 30, 2024 09:39
@jfy133 jfy133 merged commit 20be423 into dev May 30, 2024
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@jfy133 jfy133 deleted the add-krakenuniqbuild branch May 30, 2024 09:51
@jfy133 jfy133 mentioned this pull request May 30, 2024
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