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Fix BAM grouping failure due to lane field in metadata#70

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RaqManzano wants to merge 3 commits intodevfrom
fix-grouping-after-map
Open

Fix BAM grouping failure due to lane field in metadata#70
RaqManzano wants to merge 3 commits intodevfrom
fix-grouping-after-map

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@RaqManzano
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@RaqManzano RaqManzano commented Feb 17, 2026

Problem:

DNA BAMs were not progressing past the groupTuple() operation, causing the pipeline to hang indefinitely. The issue affected DNA samples with multiple lanes (L001, L002, L003). The issue was as follows:

  1. The groupTuple() operator groups items by the entire metadata map, not just some fields
  2. The lane field was still present in the metadata when creating the groupKey.
  3. This caused BAMs from the same sample to be split into separate groups based on their lane and not progress as they did not meet the condition to continue (based on the expected number of BAM files).

Solution:

Remove the lane field from metadata in the appropriate local subworkflow (BAM_ALIGN) before creating the groupKey, ensuring all BAMs from the same sample group together correctly regardless of lane.

@RaqManzano RaqManzano self-assigned this Feb 17, 2026
@RaqManzano RaqManzano added the bug Something isn't working label Feb 17, 2026
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nf-core-bot commented Feb 17, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
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 Feb 17, 2026

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e852619

+| ✅ 224 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 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 nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-17 10:32:49

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