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Features to add in release 2
Due by June 15, 2023•7/7 issues closedThings needed for a first release
Due by September 14, 2022•8/8 issues closed- No due date•12/12 issues closed
Add subworkflow for the SV block of the flowchart. - [ ] cnvpytor- a python wrapper for cnvnator with additional features calculating b-allele frequency (https://github.com/nf-core/raredisease/issues/56) - [x] manta (module already exists in nf-core) - [x] tiddit/sv (module already exists in nf-core) NB: since each SV caller requires many steps before the final vcf, it's beneficial to have them as their own individual subworkflows and THEN add them in a big "workflow". I've made a work-in-progress branch for this: https://github.com/Clinical-Genomics/raredisease/tree/feature/call_structural_variants
No due date•13/13 issues closedAdd subworkflow for the QC block of the flowchart. - [ ] Chanjo sexcheck - [ ] Samtools subsample MT - [x] Tiddit (https://github.com/nf-core/modules/issues/792) - [x] Picardtools collect multiple metrics - [x] Picardtools collect hs metrics (https://github.com/nf-core/modules/issues/793)
No due date•6/6 issues closedCreate modules for Sentieon tools (mapping, variant calling, variant filtering). Create Sentieon sub-workflow (from mapping to variant filtering). Prepare a configuration file for Sentieon license.
No due date•5/5 issues closedAnnotate SNVs
No due date•5/5 issues closedAdd some content to this repo of opportunity ## Test data Read-up and set up a test data repo. Try to use testdata that is already available ## Modules Use available nf-core when possible - BWA mem - Samtools - Markduplicates - Deepvariant - Glnexus
No due date•11/11 issues closed