[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 Mutect2 + Battenberg + DPClust seeds [HSNC single-region]
Closes #67
Pipeline Run Results
Example
sample:
ILHNLNEV000001-T001-P01-F
seed:51404
input SNV (Mutect2):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/SNV/mutect2/recsnv/vcfs/ILHNLNEV000001-T001-P01-F.vcf
input CNA (Battenberg):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/ILHNLNEV000001-T001-P01-F/ILHNLNEV000001-T001-P01-F_cellularity_ploidy.txt
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/ILHNLNEV000001-T001-P01-F/ILHNLNEV000001-T001-P01-F_subclones.txt
config:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-dpclust/input/config/seed_51404.config
yaml:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/mutect2_battenberg_yamls/single-region/ILHNLNEV000001-T001-P01-F.yaml
output:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-dpclust/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/DPClust-75f5d7e/output/ILHNLNEV000001-T001-P01-F_DPoutput_2000iters_1000burnin_seed51404/
logs:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-dpclust/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.