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Nf test #51

Merged
merged 4 commits into from
Apr 24, 2024
Merged

Nf test #51

merged 4 commits into from
Apr 24, 2024

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danilodileo
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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/magmap 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).

I added nf-test following metatdenovo

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github-actions bot commented Apr 24, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 1a5a30d

+| ✅ 169 tests passed       |+
!| ❗  31 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

  • files_unchanged - docs/images/nf-core-magmap_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-magmap_logo_dark.png does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • 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: Add full-sized test dataset and amend the paragraph below if applicable
  • 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: 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 output.md: Write this documentation describing your workflow's output
  • 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 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_description - Ungrouped param in schema: genomeinfo
  • schema_description - Ungrouped param in schema: indexes
  • schema_description - Ungrouped param in schema: ncbi_genome_infos
  • schema_description - Ungrouped param in schema: gtdb_metadata
  • schema_description - Ungrouped param in schema: checkm_metadata
  • schema_description - Ungrouped param in schema: gtdbtk_metadata
  • schema_description - Ungrouped param in schema: clip_r1
  • schema_description - Ungrouped param in schema: clip_r2
  • schema_description - Ungrouped param in schema: three_prime_clip_r1
  • schema_description - Ungrouped param in schema: three_prime_clip_r2
  • schema_description - Ungrouped param in schema: trim_nextseq
  • schema_description - Ungrouped param in schema: save_trimmed
  • schema_description - Ungrouped param in schema: skip_trimming
  • schema_description - Ungrouped param in schema: skip_qc
  • schema_description - Ungrouped param in schema: skip_fastqc
  • schema_description - Ungrouped param in schema: sourmash
  • schema_description - Ungrouped param in schema: ksize
  • schema_description - Ungrouped param in schema: bbmap_minid
  • schema_description - Ungrouped param in schema: sequence_filter
  • schema_description - Ungrouped param in schema: save_bam

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-04-24 09:57:49

erikrikarddaniel
erikrikarddaniel approved these changes Apr 24, 2024
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👍

@danilodileo danilodileo merged commit f4000f6 into nf-core:dev Apr 24, 2024
3 of 4 checks passed
@danilodileo danilodileo deleted the nf-test branch April 25, 2024 09:22
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@danilodileo @erikrikarddaniel