Add SomaticSniper-Battenberg-DPClust-SR submission script

[philsteinberg]

Description

Launch SomaticSniper + Battenberg + PyClone-VI seeds [HSNC single-region]

Closes #58

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-dpclust/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-dpclust/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/DPClust-75f5d7e/output/

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

[philsteinberg]

In your CHANGELOG it seems like you have the lines from #77. When you create a new branch, it is always best to create it from main (instead of from another branch that has commits in addition to main) so you don't accidently trip yourself lol.

Here I would recommend removing the duplicated lines with the other PR, and merging the other one first to avoid any troubles XD

I think this happened because I did command z on CHANGELOG and accidentally saved while on the new branch ... I knew something was gonna get a little messy! Trying to be diligent about creating new branches from main :)