Phils parse pipeline output #44
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@philsteinberg Please pay attention during lab meeting :) |
lydiayliu
reviewed
Aug 4, 2022
added 2 commits
August 4, 2022 12:04
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Going to adapt this code for DPClust and Issue #45 in a different PR |
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Description
Anna and I developed a script to parse the Strelka2-Battenberg-PyClone-Vi pipeline output. (Can be adapted to DPClust once that is completey finished runnning).
We dynamically read in all the output files and extract
patient,seed, and calculatenumber of subclonesand summarized that data for all patient x seed combinations in a table.Closes #38
The summary table can be found here:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-pyclone-vi/output/<date>all_subclones_per_patient_seed.tsvChecklist
I have read the code review guidelines and the code review best practice on GitHub check-list.
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].
I have added the major changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have filled in pipeline run and/or analysis resulting using the template provided above.