Add parameter glimpse version - #308
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LouisLeNezet
marked this pull request as ready for review
September 3, 2026 12:28
atrigila
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Sep 4, 2026
atrigila
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atrigila
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Nice work! Just some comments
| normalize = true | ||
| compute_freq = false | ||
| phase = false | ||
| chunk_version = "V2" |
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Can you update usage.md to document these new changes, please? Thank you :)
| compute_freq : params.compute_freq, | ||
| phase : params.phase, | ||
| chunk_model : params.chunk_model | ||
| chunk_model : params.chunk_model, |
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Chunk model won't apply to both v1 and v2, right? Should we have a warning if you provide a v2 model and request a v1 version?
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Maybe a test case can be added to cover for this scenario as well
| GLIMPSE2_CHUNK(ch_input_glimpse2, chunk_model) | ||
| ch_chunks = GLIMPSE2_CHUNK.out.chunk_chr | ||
| } else { | ||
| error ("Parameter chunk_version should be V1 or V2, found: ${chunk_version}.") |
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I think this is not needed since it should fail before this if a different one is provided. It should fail and error due to the schema which only allows enums.
| if (row.size() == 8) { | ||
| return [ meta, row[3], row[2] ] // header is 'ID', 'Chr', 'RegionBuff', 'RegionCnk', 'WindowCm', 'WindowMb', 'NbTotVariants', 'NbComVariants' | ||
| } | ||
| error "Chunks csv should have either 6 columns (glimpse V1 format) or 8 columns (glimpse V2 format)" |
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This should also be documented in usage.md
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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).