Add low-pass bam/vcf and genetic map #1796
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hmm, this broke some tests that relied on the old file names, e.g. https://github.com/nf-core/modules/actions/runs/19709033762/job/56464494808?pr=9333#step:6:848 |
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I'm currently updating them |
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I think the easier move would be to add the the files without removing old files. Or was there something wrong with them? |
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The aim was to avoid to have the same file with two or only one chromosome. |
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@LouisLeNezet , why was this deleted?
This has broken sarek tests:
https://github.com/nf-core/sarek/actions/runs/19706542568/job/56455675487?pr=2060#step:4:1381
as well as presumably two modules (cnvnator/cnvnator and cnvnator/convert2vcf)
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should we just add the old files back (with a fixed map)?
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I'm really sorry. That it broke sarek pipeline.
I will add back the chr22 only files.
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I've updated the two other modules.
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thank you! don't want to rewrite all tests for the upcoming release
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could you also add the vcf files back? That broke a subworkflow test https://github.com/nf-core/modules/actions/runs/19733276765/job/56539345421?pr=9333#step:6:1304
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This PR add bam and vcf file for two individuals on two chromosomes to simulate low-pass data.
Genetic map in various format for the different imputation tools are also added as well as the reference panel for the two chromosomes.