DEV - Switch reference genome to hg38 for raredisease#4871
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DEV - Switch reference genome to hg38 for raredisease#4871
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dnil
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Feb 4, 2026
dnil
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Feb 4, 2026
Co-authored-by: Daniel Nilsson <daniel.k.nilsson@gmail.com>
change raredisease genome version for bed version fetch to hg38 --------- Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
Use Scout38 in the ConfiguratorFactory for the creation of managed_variants and gene_panel files for raredisease --------- Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com> Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
* use scout_api_38 for rd * WIP * coverage for create scout config * make raredisease get scout 38 for upload * parametrize test checking scout instance per workflow * WIP integration test * fix faulty imports * wip * Remove integration test - will be done in another PR * Add todo * More TODOs * Change rd scout link in delivery report template and add test assertion * wip * fix todo, parametrize get_scout_api * fix todo * WIP * Instantiation complete * fix test * remove unused kwargs --------- Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com> Co-authored-by: Sebastian Diaz <juan.sebastian.diaz.boada@scilifelab.se> Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>
* wip * Start writing test * Golden green state * parametrize * fix type hint * adress comments --------- Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se> Co-authored-by: islean <isak.ohlsson.angnell@gmail.com>
* added rd to parametrization, passing * expand fixtures * generalize, still can't generalize nallo_case fixture * simplify test * try using string templates for the message fixtures * use format strings instead of string.Template
* WIP * Finish implementation minus instantiation * Loose end: Fix instantiations of RarediseaseParamsFileCreator missing config and failing tests (#4904) * fix instantiations and failing tests * fix faulty import path, now only the tests for the implementation should be failing * Golden green * Golden green * WIP * golden green renaming * added new test, red state * Golden green * Raredisease classes * Rename raredisease_params_file_creator add to cg-test.yaml --------- Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Alfred Kedhammar <89784800+kedhammar@users.noreply.github.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se>
Add germlinecnv-caller configs --------- Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>
Closes: Clinical-Genomics/RD-hg38#10 Prefix target_bed with references directory, default bed when missing in LIMS --------- Co-authored-by: Rasmus Burge <80392398+RasmusBurge-CG@users.noreply.github.com>
Rename mutacc commands and add --genome-version flag to specify version of mutacc --------- Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>
* WIP * Remove MAF case creation * Starting to remove genotype * Removed upload in GenotypeAPI * Started removing upload func in UploadGenotypesAPI * Remove the last genotype API * Update READMEs, remove unused fixtures * Update vulture whitelist --------- Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>
* [hg38] Update RNA uploads * Add TODO * add tests checking genome build against scout build and remove duplicate test * golden * use sets * WIP * task failed successfully * Refactor test * Update tests * WIP * SILVER - GOLDEN --------- Co-authored-by: islean <isak.ohlsson.angnell@gmail.com> Co-authored-by: kedhammar <alfred.kedhammar@scilifelab.se> Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com> Co-authored-by: Linnéa Löfdahl <linnea.lofdahl@scilifelab.se>
diitaz93
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Mar 13, 2026
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cg/services/analysis_starter/configurator/file_creators/nextflow/utils.py
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| (Workflow.BALSAMIC, "scout_api_37"), | ||
| (Workflow.BALSAMIC_UMI, "scout_api_37"), | ||
| (Workflow.MIP_DNA, "scout_api_37"), | ||
| (Workflow.MIP_RNA, "scout_api_37"), |
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Maybe RNA pipelines don't belong to this parametrisation because they don't use this command, I will investigate
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possibly remove RNA pipelines from this parametrisation
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tests/services/analysis_starter/file_creators/test_gene_panel_file_creator.py
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RIP genotype 🪦 Looks good! I can't approve my own PR. I am confused when RNA has HG19 and when HG38
### Changed - skip_germlinecnvcaller reworked into skip_tools
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Servers PR: https://github.com/Clinical-Genomics/servers/pull/1802
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