Add new parser for FACETS

uclahs-cds / project-method-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed

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Add new parser for FACETS #22

Open lydiayliu opened 2 years ago

lydiayliu commented 2 years ago

FACETS

github: https://github.com/mskcc/facets
paper: https://academic.oup.com/nar/article/44/16/e131/2460163
test data: /hot/software/pipeline/pipeline-call-SRC/Nextflow/development/test_inputs/data/SARC0121_DMSO/facets/

lydiayliu commented 2 years ago

Sorry @ANeimanGolden I changed my mind. We want to have pipeline-call-SRC take the FACETS standard output from running call-sCNA. Since I didn't run FACETS using the call-sCNA pipeline, I don't have the correct input for this for the head and neck cohort (which will be used to run with different seeds). Could we switch the priority to Battenberg instead? https://github.com/uclahs-cds/project-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed/issues/21 Sorry about this!!

ANeimanGolden commented 2 years ago

Got it, I'll take a look.

lydiayliu commented 1 year ago

More test data here /hot/user/amarkowitz/Rhabdomyoma/pipeline/call-sCNA/