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Allow all tool's databases to be provided as .tar.gz files #219

Merged
merged 7 commits into from
Jan 25, 2023
Merged

Allow all tool's databases to be provided as .tar.gz files #219

merged 7 commits into from
Jan 25, 2023

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jfy133
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@jfy133 jfy133 commented Jan 24, 2023

Even if it doesn't make sense (e.g. with diamond), but there for consistency

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).

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github-actions bot commented Jan 24, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c765b3f

+| ✅ 157 tests passed       |+
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • 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.
  • 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 taxprofiler.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-01-24 14:32:43

@jfy133 jfy133 requested a review from a team January 24, 2023 09:58
@jfy133 jfy133 mentioned this pull request Jan 24, 2023
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Midnighter
Midnighter requested changes Jan 24, 2023
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Sorry, I can't allow you to merge the error strategy change here when that's part of the other PR. Otherwise it looks good to me with a small suggestion.

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jfy133 commented Jan 24, 2023

I confirm it works locally 👍

@jfy133 jfy133 merged commit 47efd19 into dev Jan 25, 2023
@jfy133 jfy133 deleted the allow-targz-motus branch January 25, 2023 12:48
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