Standardize Repo

[Faizal-Eeman]

Description

Standardize repo, before request is made to make this repo public.

Closes #2

Docker image testing

Build log: /hot/software/image/docker-Manta/Docker/development/1.6.0/manta-1.6.0-build.log

My command:
docker run -it --rm -u $(id -u):$(id -g) -w $(pwd) manta:v1.6.0 configManta.py --help

Usage: configManta.py [options]

Version: 1.6.0

This script configures the Manta SV analysis pipeline.
You must specify a BAM or CRAM file for at least one sample.

Configuration will produce a workflow run script which
can execute the workflow on a single node or through
sge and resume any interrupted execution.

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  --config=FILE         provide a configuration file to override defaults in
                        global config file (/usr/local/share/manta-1.6.0-2/bin
                        /configManta.py.ini)
  --allHelp             show all extended/hidden options

Checklist

• This PR does NOT contain Protected Health Information (PHI). A repo may need to be deleted if such data is uploaded.
  Disclosing PHI is a major problem¹ - Even a small leak can be costly².

• This PR does NOT contain germline genetic data³, RNA-Seq, DNA methylation, microbiome or other molecular data⁴.

• This PR does NOT contain other non-plain text files, such as: compressed files, images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other output files.

  To automatically exclude such files using a .gitignore file, see here for example.

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

• I have set up or verified the main branch protection rule following the github standards before opening this pull request.

• 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.md under the next release version or unreleased, and updated the date.

Footnotes

1. UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records ↩

2. The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records. ↩

3. Genetic information is considered PHI.
   Forensic assays can identify patients with as few as 21 SNPs ↩

4. RNA-Seq, DNA methylation, microbiome, or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity. ↩

[yashpatel6]

Looks good!

[yashpatel6]

Newline

[wiz-inc-8da00b022c]

Wiz Scan Summary

IaC Misconfigurations
Vulnerabilities
Sensitive Data
Total
Secrets