Add parameter glimpse version - #308
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LouisLeNezet
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September 3, 2026 12:28
atrigila
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Sep 4, 2026
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Nice work! Just some comments
| 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
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We were providing the default sequential model for glimpse2.
So I added a error message if the model provided is different to the default when V1 is selected.
We could also set --chunk_model to null and give an error when V2 is selected with no model.
| 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.
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I agree, that it should already failed thanks to nextflow.schema.
But, if a some point we share this subworkflow, I'd prefer that it verify that the format is correct.
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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).