Add SomaticSniper-Battenberg-PhyloWGS-sr submission script

[philsteinberg]

Description

Launch SomatiSniper + Battenberg + PhyloWGS + seeds [HSNC single-region] Seed + Sample combination that does not work due to mcmc number https://github.com/uclahs-cds/project-method-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed/issues/63

Changed /hot/users/psteinberg/git/project-SRC-RandomSeed/src/output-analysis/parsing/run_parse_consensus_tree_PhyloWGS.sh to parse SomaticSniper-Battenberg-PhyloWGS output.

Closes #63

Pipeline Run Results

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-phylowgs/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 (split between two output folders): /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/

• PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg-mutass.json.gz
• PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg-muts.json.gz
• PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg-summ.json.gz

/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.1.0/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output

• PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg.mutass.json.gz
• PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg.muts.json.gz
• PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg.summ.json.gz

logs: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/logs/

witness data: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/witness_results/

Consensus (best) tree output: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/consensus_tree

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.