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Add bam/cram support #157

Merged
merged 8 commits into from
Jan 8, 2025
Merged

Add bam/cram support #157

merged 8 commits into from
Jan 8, 2025
+1,444 −61

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nvnieuwk
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@nvnieuwk nvnieuwk commented Jan 7, 2025 •
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Add support for BAM/CRAM input (fixes #41)

Following steps were added:

  1. Add new samplesheet fields: bam, bai, cram, crai
  2. Add additional checks to prevent weird issues caused by having multiple input file types
  3. Optionally create the index of the file when missing
  4. Add the alignment files to the flow right before GATK4_SPLITNCIGARREADS

There are still some things left to do:

  • Update the changelog
  • Add and update the tests

@nvnieuwk nvnieuwk requested a review from maxulysse January 7, 2025 15:29
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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 Jan 7, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c788544

+| ✅ 225 tests passed       |+
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 base.config: Check the defaults for all processes

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-08 13:30:02

maxulysse
maxulysse reviewed Jan 7, 2025
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Looking good, but need to check the snapshots

@nvnieuwk
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nvnieuwk commented Jan 7, 2025

Looking good, but need to check the snapshots

Currently working on that ;)

@nvnieuwk nvnieuwk merged commit afd9ff2 into nf-core:dev Jan 8, 2025
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@nvnieuwk nvnieuwk deleted the add-bam/cram-support branch January 8, 2025 13:49
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@maxulysse maxulysse maxulysse approved these changes

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@nvnieuwk @nf-core-bot @maxulysse