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35 Open 91 Closed
35 Open 91 Closed
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Issues list

single pipeline runs from BAM are currently broken
#313 opened Oct 14, 2024 by sorelfitzgibbon
1
Add missing processes in SomaticSniper to resource configs enhancement New feature or request
#305 opened Jul 6, 2024 by tyamaguchi-ucla
@sorelfitzgibbon
Create separate workflows for each input type
#296 opened May 29, 2024 by sorelfitzgibbon
Add example doc with CPU/Mem resources for very large samples
#288 opened May 10, 2024 by Faizal-Eeman
8
Update contamination table instructions in README
#286 opened May 6, 2024 by sorelfitzgibbon
Additional Benchmarking to be added to README?
#285 opened Apr 30, 2024 by sorelfitzgibbon
1
Update repository description to match standard standardization
#283 opened Apr 11, 2024 by nwiltsie
standardize input structure
#278 opened Mar 12, 2024 by sorelfitzgibbon
1
Add option to input 2 or more VCFs for intersection.
#273 opened Feb 14, 2024 by sorelfitzgibbon
2 of 5 tasks
@sorelfitzgibbon
simplifiy samples_to_process handling
#253 opened Dec 1, 2023 by sorelfitzgibbon
move params.germline... out of methods.config
#252 opened Dec 1, 2023 by sorelfitzgibbon
remove use_intersect_regions throughout since intersect_regions are required
#251 opened Dec 1, 2023 by sorelfitzgibbon
move set_sample_params to main.nf
#250 opened Dec 1, 2023 by sorelfitzgibbon
Resources for single algorithm runs
#243 opened Oct 20, 2023 by sorelfitzgibbon
Add assertions for 2 and 3 tool combinations
#238 opened Oct 2, 2023 by sorelfitzgibbon
Some parameters are required even when the relevant algorithm is not being run
#227 opened Aug 16, 2023 by sorelfitzgibbon
think about structure under intersect-BCFtools-1.17
#221 opened Aug 10, 2023 by sorelfitzgibbon
Adding a time limit for MuSE
#220 opened Aug 9, 2023 by maotian06
Parameterize the VennDiagram version
#219 opened Aug 2, 2023 by sorelfitzgibbon
create canonical chrs output VCF?
#217 opened Aug 1, 2023 by sorelfitzgibbon
update to BCFtools 1.18 and adjust pipeline to use auto indexing
#212 opened Jul 25, 2023 by sorelfitzgibbon
The headers of the output VCFs still contain removed contigs
#209 opened Jul 17, 2023 by sorelfitzgibbon
add by-chr QC plot
#207 opened Jul 17, 2023 by sorelfitzgibbon
@sorelfitzgibbon
modularize the intersection process
#200 opened Jul 14, 2023 by sorelfitzgibbon
@sorelfitzgibbon
Update Issue Template
#194 opened Jun 28, 2023 by tyamaguchi-ucla
@sorelfitzgibbon
ProTip! Updated in the last three days: updated:>2024-11-11.