Add TCR genotyping support and update documentation - #482
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- Introduced new configuration for TCR genotyping tests. - Updated the main workflow to handle both IG and TR loci for genotype inference. - Enhanced documentation to clarify the functionality and parameters related to TCR genotyping. - Adjusted JSON schema descriptions for clarity on genotype inference processes.
ggabernet
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Jul 27, 2026
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Just a comment, otherwise looks good to me. Since the logic is quite complex now, it would be good to add a test case where there are mixed loci repertoires, and from different genotypeby groups, to ensure the repertoires and references are joined properly.
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| ch_repertoires_for_grouping | ||
| .map{ it -> [it[0], it[1]] } | ||
| .groupTuple() | ||
| .map{ it -> [it[0], it[1].unique().size() > 1] } | ||
| .set{ ch_mixed_locus_by_genotype } | ||
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| ch_repertoires_for_grouping | ||
| .map{ it -> [it[0], it] } | ||
| .join(ch_mixed_locus_by_genotype) | ||
| .map{ it -> | ||
| def entry = it[1] | ||
| def mixed_locus = it[2] | ||
| [ [entry[0], entry[1]], | ||
| entry[2], | ||
| entry[3], | ||
| entry[4], | ||
| entry[5], | ||
| entry[6], | ||
| entry[7], | ||
| entry[8], | ||
| entry[9], | ||
| mixed_locus ] } |
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I'm not following why this is needed. Can't you just groupTuple once like the previous implementation, using
.groupTuple(by: [0,1])
So it will group by both genotypeby and locus, then use the branching as you do below. I think this would be a simpler solution.
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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: 4.0.2. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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ggabernet
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Aug 10, 2026
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Looks good to me, let's check that all tests are passing now that GHA is working again
❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
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Some tests seem to be failing due to a reassign alleles specific thing. One test was failing due to the appending of the |
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The first fail will be resolved with the PR merge to enchantr |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).