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Checksum verification #10

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@grst grst commented Dec 11, 2024

Close #2

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/datasync branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

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github-actions bot commented Dec 11, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit fc39629

+| ✅ 187 tests passed       |+
!| ❗  22 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • modules_config - conf/modules.config contains withName:FASTQC, but the corresponding process is not present in any of the Nextflow scripts.

❗ 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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: 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • 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 main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • schema_description - No description provided in schema for parameter: workflow_type
  • schema_description - No description provided in schema for parameter: chunksize

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-02-06 13:06:39

grst added 3 commits December 11, 2024 14:38
@grst
Fix smaplesheet verification
339fda2
@grst
WIP: Only stage necessary files
b2b17fa 
This branch is an attempt to only stage the necessary files.
This would be very efficient on S3, but it's also rather complicated
and involves a lot of hacks. It is also unnecessary on systems
with a shared files system or fusion.
@grst
Implement chunking
924ce82
@nf-core-bot
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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@grst grst changed the title POC Checksum verification Checksum verification Dec 16, 2024
@grst grst marked this pull request as ready for review December 16, 2024 08:21
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Data Integrity Checking feature
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@grst @nf-core-bot