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Adding pipeline nf-tests to nf-core/mag #550

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Adding pipeline nf-tests to nf-core/mag #550

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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/mag 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 and others added 15 commits September 26, 2023 10:59
@jfy133
Merge pull request nf-core#499 from nf-core/dev
18a1645 
Release 2.4
@jfy133
Merge pull request nf-core#524 from nf-core/dev
ba72349 
Release: 2.5.0
@jfy133
Merge pull request nf-core#541 from nf-core/dev
e728900 
Patch release 2.5.1
@CarsonJM
Added ability to auto-create samplesheet for phageannotator
65034b5
@CarsonJM
Created tests for samplesheet creation
43491d8
@CarsonJM
Added nf-core-pipeline parameter to schema
e39111e
@CarsonJM
Changed input to samplesheet creation
69c684e
@CarsonJM
Conditional running of samplesheet creation
bd06532
@CarsonJM
Updated docs and added pipeline to output file name
a564425
@CarsonJM
Started structuring mag for nf-tests
11bc721
@CarsonJM
Moving config file params to nf-test files
f97ef32
@CarsonJM
virus identification test complete
53e58e1
@CarsonJM
Added test_adapterremoval tests
4dc19db
@CarsonJM
Merge branch 'pipeline-nf-tests' of https://github.com/CarsonJM/mag i…
848f4ef 
…nto pipeline-nf-tests
@CarsonJM
Merge branch 'nf-core:master' into pipeline-nf-tests
d5ec5e4
@CarsonJM CarsonJM changed the base branch from master to dev December 13, 2023 00:58
@nf-core nf-core deleted a comment from github-actions bot Dec 13, 2023
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github-actions bot commented Dec 13, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 41c682a

+| ✅ 209 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in WorkflowMag.groovy: Optionally add in-text citation tools 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
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-14 19:09:09

@CarsonJM CarsonJM added the WIP Work in progress label Dec 13, 2023
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@nf-core-bot fix linting

@CarsonJM CarsonJM self-assigned this Feb 9, 2024
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@CarsonJM @jfy133 @nf-core-bot