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Adopt nft-utils #182

Merged
merged 17 commits into from
Dec 21, 2024
Merged

Adopt nft-utils #182

merged 17 commits into from
Dec 21, 2024

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edmundmiller
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@edmundmiller edmundmiller commented Dec 15, 2024 •
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Adopts nft-utils #177 (comment)

@edmundmiller edmundmiller self-assigned this Dec 15, 2024
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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.

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github-actions bot commented Dec 15, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3b9ee15

+| ✅ 219 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in base.config: Check the defaults for all 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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • actions_ci - actions_ci

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-12-21 03:50:59

@edmundmiller edmundmiller added this to the 2.3.0 milestone Dec 15, 2024
@edmundmiller edmundmiller force-pushed the nft-utils branch 3 times, most recently from ba256f1 to 77b5eec Compare December 16, 2024 04:43
@edmundmiller
test: Skip bam checks
5404d64 
I'll fix this with the cram file publishing

Remove bam files
@edmundmiller edmundmiller force-pushed the nft-utils branch 4 times, most recently from 7e3c1de to 4e08546 Compare December 19, 2024 03:57
@edmundmiller edmundmiller marked this pull request as ready for review December 21, 2024 04:21
@edmundmiller edmundmiller merged commit bb5a3a8 into dev Dec 21, 2024
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@sateeshperi sateeshperi sateeshperi approved these changes

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