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Take rnaseq preprocessing workflow from nf-core #10

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merged 7 commits into from
Feb 2, 2024

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pinin4fjords
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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/riboseq 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 Feb 1, 2024

nf-core lint overall result: Failed ❌

Posted for pipeline commit 858c289

+| ✅ 174 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  19 tests had warnings |!
-| ❌  14 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.ribo_database_manifest is set as ${projectDir}/assets/rrna-db-defaults.txt in nextflow_schema.json but is /home/runner/work/riboseq/riboseq/assets/rrna-db-defaults.txt in nextflow.config.
  • nextflow_config - Config default value incorrect: params.test_data_base is set as https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3 in nextflow_schema.json but is https://raw.githubusercontent.com/nf-core/test-datasets/riboseq/testdata/ in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-riboseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-riboseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-riboseq_logo_dark.png does not match the template
  • files_unchanged - .gitignore does not match the template
  • files_unchanged - .prettierignore does not match the template
  • files_unchanged - pyproject.toml does not match the template

❗ 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: Fill in short bullet-pointed list of the default steps in the pipeline
  • 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 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 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 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.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowRiboseq.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12.1
  • Run at 2024-02-01 18:12:50

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@adamrtalbot adamrtalbot left a comment

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At first I was scared but then I realised it wasn't actually many changes other than pulling stuff from nf-core/modules.

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Thanks @adamrtalbot !

@pinin4fjords pinin4fjords merged commit aacf8a2 into dev Feb 2, 2024
54 of 55 checks passed
@pinin4fjords pinin4fjords deleted the preprocessing_from_nfcore branch February 2, 2024 08:57
@pinin4fjords pinin4fjords linked an issue Feb 19, 2024 that may be closed by this pull request
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Define preprocessing
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