Add Strelka2-Battenberg-PyClone-VI-MR submission script

[philsteinberg]

Description

Re-Launch Strelka2 + Battenberg + PyClone-VI seeds [HSNC single-region] due to errors from parsing original sSNV output.

Closes #80

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 (Strelka2): /hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/SNV/strelka2/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-strelka2-battenberg-pyclone-vi/input/config/seed_51404.config

yaml: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/multi-region/ILHNLNEV000001.yaml

output: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-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_Strelka2-Battenberg.tsv

logs: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/logs/

Checklist

• [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 read the code review guidelines and the code review best practice on GitHub check-list.
• [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.