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Fancy checksum verification #12

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@grst grst commented Dec 12, 2024

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 added 3 commits December 11, 2024 14:06
@grst
WIP implement as local modules
f6757a1
@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.
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github-actions bot commented Dec 12, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit b2b17fa

+| ✅ 186 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 main.nf: Remove this line if you don't need a FASTA file
  • 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 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 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 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 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 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 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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 2024-12-12 12:02:07

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