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Add dorado #277

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yuukiiwa
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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/nanoseq 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).

yuukiiwa and others added 16 commits October 17, 2023 16:53
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Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@github-actions GitHub Actions
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 3d4521a

+| ✅ 214 tests passed       |+
!| ❗   6 tests had warnings |!
-| ❌  23 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowNanoseq.groovy
  • nextflow_config - Config default value incorrect: params.kit is set as `` in nextflow_schema.json but is `null` in `nextflow.config`.
  • nextflow_config - Config default value incorrect: params.flowcell is set as `` in nextflow_schema.json but is `null` in `nextflow.config`.
  • nextflow_config - Config default value incorrect: params.dorado_model is set as `` in nextflow_schema.json but is `null` in `nextflow.config`.
  • nextflow_config - Config default value incorrect: params.jaffal_ref_dir is set as for_jaffal in nextflow_schema.json but is null in nextflow.config.
  • nextflow_config - Config default value incorrect: params.tracedir is set as ${params.outdir}/pipeline_info in nextflow_schema.json but is ./results/pipeline_info in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • 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-nanoseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-nanoseq_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-nanoseq_logo_dark.png does not match the template
  • schema_params - Param input_path_file_type from nextflow config not found in nextflow_schema.json
  • schema_params - Param bedmethyl_out from nextflow config not found in nextflow_schema.json
  • schema_params - Param doraro_modification from nextflow config not found in nextflow_schema.json
  • modules_config - conf/modules.config contains withName:STRINGTIE2, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.1.0
  • 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 methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • nfcore_yml - nf-core version not set in .nf-core.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-19 09:31:22

@maxulysse maxulysse mentioned this pull request Oct 8, 2024
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2 participants
@yuukiiwa @LaurenceKuhl