[x] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
[x] This PR does NOT contain molecular files, compressed files, output files such as images (e.g..png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
[x] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
[x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
[x] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
Description
Launch SomaticSniper + Battenberg + PyClone-VI seeds [HSNC multi-region]
Closes #90
Pipeline Run Results
Example
patient:
ILHNLNEV000001
seed:51404
samples:
ILHNLNEV000001-T001-P01-F
ILHNLNEV000001-T002-P02-F
ILHNLNEV000001-T003-L01-F
ILHNLNEV000001-T004-L02-F
input SNV (SomaticSniper):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/SNV/somaticsniper/recsnv/vcfs/<samples.vcf>
input CNA (Battenberg):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/<samples>/<samples>_cellularity_ploidy.txt
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/<samples>/<samples>_subclones.txt
config:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/input/config/seed_51404.config
yaml:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/multi-region/ILHNLNEV000001.yaml
output:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001/PyClone-VI-0.1.2/output/PyClone-VI-0.1.2_51404_ILHNLNEV000001_SomaticSniper-Battenberg.tsv
logs:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-pyclone-vi/logs/
Checklist
.png
, .jpeg
),.pdf
,.RData
,.xlsx
,.doc
,.ppt
, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.main
branch protection rule following the github standards before opening this pull request.CHANGELOG.md
under the next release version or unreleased, and updated the date.