Fix FilterMutectCalls not running when starting from BAM with lane field #2124
+185
−179
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
When starting from `--step variant_calling` with BAM files that include a `lane` column in the samplesheet, the meta.id was set to `sample-lane` (e.g. "PM10_P0-1"). However, the Mutect2 tumor-only subworkflow resets the ID to `meta.sample` (e.g. "PM10_P0") at the pileup/contamination step. This mismatch caused the `.join()` to produce an empty channel, so FilterMutectCalls silently never ran. The fix uses lane-based IDs only for the mapping step (where lanes are processed separately). For all other steps, the sample-based ID is used, ensuring consistent ID matching in downstream channel joins. Co-Authored-By: Claude Opus 4.6 <[email protected]>
Co-Authored-By: Claude Opus 4.6 <[email protected]>
Member
|
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. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Co-Authored-By: Claude Opus 4.6 <[email protected]>
|
maxulysse
reviewed
Feb 9, 2026
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Summary
--step variant_callingwith BAM files that include alanecolumn in the samplesheet,FilterMutectCallssilently does not run, causing variants to not be annotated/filteredmeta.idwas set tosample-lane(e.g.,"PM10_P0-1") in samplesheet parsing, but the Mutect2 tumor-only subworkflow resets the pileup/contamination ID tometa.sample(e.g.,"PM10_P0"), causing.join()mismatches that produce empty channelsFixes the issue where removing the
lanefield from the samplesheet was the only workaround.Test plan
--step variant_callingwith BAM input withlanefield in samplesheet — verifyFilterMutectCallsruns--step variant_callingwith BAM input withoutlanefield — verify no regression--step mappingwith BAM input withlanefield — verify alignment still uses lane-based IDs🤖 Generated with Claude Code