[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.
Yash sent me the link to the submission script he is developing, but he said it is still under review. Therefore I am submitting the scripts I used for the already completed pipelines.
Description
Launch SomaticSniper + Battenberg + PyClone-VI seeds [HSNC single-region]
Closes #57
Pipeline Run Results
Example
sample:
ILHNLNEV000001-T001-P01-F
seed:51404
input SNV (SomaticSniper):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/SNV/somaticsniper/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-somaticsniper-battenberg-pyclone-vi/input/config/seed_51404.config
yaml:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/ILHNLNEV000001-T001-P01-F.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-T001-P01-F/PyClone-VI-0.1.2/PyClone-VI-0.1.2_51404_ILHNLNEV000001-T001-P01-F_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.