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Blatbox #14

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edmundmiller
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Quick PoC workflow I threw together. I plan on building starting from bams.

@edmundmiller edmundmiller self-assigned this May 16, 2022
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github-actions bot commented May 16, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit e9ee50b

+| ✅ 141 tests passed       |+
!| ❗  19 tests had warnings |!
-| ❌   7 tests failed       |-

❌ Test failures:

  • nextflow_config - Config dag.file did not end with .html
  • 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
  • schema_params - Param skip_alignment from nextflow config not found in nextflow_schema.json
  • schema_params - Param bwa_index from nextflow config not found in nextflow_schema.json

❗ 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: 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run 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 blatbox.nf: Add all file path parameters for the pipeline to the list below
  • pipeline_todos - TODO string in viralintegration.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 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.

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-05-23 16:04:01

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