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LouisLeNezet
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Apr 20, 2026
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LouisLeNezet
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Just a few small changes, but good to go otherwise !
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| ch_versions = ch_versions.mix(QUILT_QUILT2.out.versions_r_quilt) | ||
| ch_versions = ch_versions.mix(QUILT_QUILT2.out.versions_r_base) |
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Shouldn't QUILT2 use topics for that ?
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| withName: BCFTOOLS_INDEX { | ||
| ext.args = "--tbi" | ||
| publishDir = [enabled: false] |
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I don't think publishDir is necessary for the unittest
| tag "glimpse2" | ||
| tag "glimpse2/ligate" | ||
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| test("Impute with quilt2 one individual, one region, map and fasta") { |
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Could you add the optional bamnames input file to ensure it does work properly.
This file will be necessary for phaseimpute to work with simulated data at the validation step.
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json | ||
| name: "bam_impute_quilt2" | ||
| description: | | ||
| Impute low-coverage BAM or CRAM inputs with QUILT2 and ligate chunked outputs per chromosome. |
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Could you just add a line to explain that the regionout key will be used to store temporarily the region and therefore shouldn't be used in the meta maps ?
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PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda