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nf-validation plugin for samplesheet validation #7

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wants to merge 8 commits into from
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nf-validation plugin for samplesheet validation #7

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LilyAnderssonLee
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Close issues #3 #5

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/metaval 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).

@LilyAnderssonLee
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The raw test data was downloaded from the article A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification including three Illumina samples and one Nanopore sample.
Illumina samples: SRR13439790; SRR13439802; SRR13439813
Nanopore sample: SRR13439799

sofstam
sofstam requested changes Jan 8, 2024
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@sofstam sofstam left a comment

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Nice! Good to set up some actions? Similar to taxprofiler or https://github.com/genomic-medicine-sweden/tomte/actions.

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@LilyAnderssonLee
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I have enabled github Action and will add CI test later.

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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!

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github-actions bot commented Jan 17, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit c3e4b6e

+| ✅ 157 tests passed       |+
!| ❗  19 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • 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/linting.yml does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/metaval/tree/dev" target="_blank">nf-core/metaval</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/metaval/dev/docs/output" target="_blank">documentation</a>.
    The current comment is:
    This report has been generated by the <a href="https://github.com/nf-core/metaval/releases/tag/dev" target="_blank">nf-core/metaval</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/metaval/dev/docs/output" target="_blank">documentation</a>.

❗ 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 nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • 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 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 output.md: Write this documentation describing your workflow's output
  • 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 WorkflowMetaval.groovy: Optionally add in-text citation tools to this list.
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-17 11:55:58

@LilyAnderssonLee LilyAnderssonLee deleted the input branch February 8, 2024 13:40
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@sofstam sofstam sofstam requested changes

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@LilyAnderssonLee @sofstam