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Add DatabaseSearchEngines Subworkflow #14

Merged
merged 3 commits into from
Nov 13, 2021
Merged

Add DatabaseSearchEngines Subworkflow #14

merged 3 commits into from
Nov 13, 2021

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daichengxin
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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/quantms 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).
  • 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 Nov 11, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 018c34d

+| ✅ 136 tests passed       |+
!| ❗  15 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
  • 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: Update the example "typical command" below used to run the pipeline
  • 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 ci.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-11-13 08:51:39

@ypriverol ypriverol self-requested a review November 12, 2021 07:33
@ypriverol ypriverol merged commit 9dde645 into bigbio:dev Nov 13, 2021
@ypriverol ypriverol mentioned this pull request Nov 14, 2021
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ypriverol pushed a commit that referenced this pull request Aug 2, 2022
@daichengxin
Merge pull request #14 from bigbio/dev
527d004 
u
daichengxin added a commit that referenced this pull request Mar 24, 2024
@daichengxin
Merge pull request #14 from daichengxin/nf-template-12
77f4ce0 
Nf template 12
mobiusklein pushed a commit to mobiusklein/quantms that referenced this pull request Aug 9, 2024
@ypriverol
Merge pull request bigbio#14 from bigbio/dev
3796297 
Dev
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@ypriverol ypriverol ypriverol approved these changes

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@daichengxin @ypriverol