Initial release

.github/pull_request_template.md

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+# Description
+<!--- Briefly describe the changes included in this pull request  --->
+
+### Closes #...  <!-- edit if this PR closes an Issue -->
+
+# Checklist
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
+
+- [ ] This PR **does *NOT* contain** Protected Health Information [(PHI)](https://ohrpp.research.ucla.edu/hipaa/). A repo may ***need to be deleted*** if such data is uploaded. <br> Disclosing PHI is a ***major problem***[^1] - Even ***a small leak can be costly***[^2].
+
+- [ ] This PR **does *NOT* contain** germline genetic data[^3], RNA-Seq, DNA methylation, microbiome or other molecular data[^4].
+
+[^1]: [UCLA Health reaches $7.5m settlement over 2015 breach of 4.5m patient records](https://healthitsecurity.com/news/ucla-health-reaches-7.5m-settlement-over-2015-breach-of-4.5m)
+[^2]: [The average healthcare data breach costs $2.2 million, despite the majority of breaches releasing fewer than 500 records.](https://www.ponemon.org/local/upload/file/Sixth%20Annual%20Patient%20Privacy%20%26%20Data%20Security%20Report%20FINAL%206.pdf)
+[^3]: [Genetic information is considered PHI.](https://www.genome.gov/about-genomics/policy-issues/Privacy#:~:text=In%202013%2C%20as%20required%20by,genetic%20information%20for%20underwriting%20purposes.)
+  [Forensic assays can identify patients with as few as 21 SNPs](https://www.sciencedirect.com/science/article/pii/S1525157817305962)
+[^4]: [RNA-Seq](https://www.nature.com/articles/ng.2248), [DNA methylation](https://ieeexplore.ieee.org/document/7958619), [microbiome](https://www.pnas.org/doi/pdf/10.1073/pnas.1423854112), or other molecular data can be used to predict genotypes (PHI) and reveal a patient's identity.
+
+
+- [ ] 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.
+
+_&emsp; To automatically exclude such files using a [.gitignore](https://docs.github.com/en/get-started/getting-started-with-git/ignoring-files) file, see [here](https://github.com/uclahs-cds/template-base/blob/main/.gitignore) for example._
+
+- [ ] I have read the [code review guidelines](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3187646/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List).
+
+- [ ] I have set up or verified the `main` branch protection rule following the [github standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190380/GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request.
+
+- [ ] The name of the branch is meaningful and well formatted following the [standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3189956/Code+Review+Best+Practice+on+GitHub+-+Check+List), 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.

.github/workflows/static-analysis.yml

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+---
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  static-analysis:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: uclahs-cds/tool-static-analysis@v1

.gitignore

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+# System files
+*.log
+.DS_Store
+
+# R
+.Rhistory
+.Rapp.history
+.Rproj.user
+*.RData
+*.rd[as]
+
+# Python
+__pycache__/
+.pytest_cache/
+.Python
+pip-log.txt
+pip-delete-this-directory.txt
+*.py[cod]
+*$py.class
+venv
+.venv
+.env
+
+# VScode
+.vscode
+
+# Nextflow
+work/
+.nextflow/
+*.nextflow.log*
+
+## Molecular files
+
+# Array file
+*.CEL
+*.cel
+*.OSCHP
+
+# Sequence file (e.g. Reference genome)
+*.fasta
+*.fa
+*.fai
+*.dict
+*.gtf
+
+
+# FASTQ file
+*.fq
+*.fastq
+
+# Proteomics file
+*.raw
+*.mzML
+*.mzXML
+*.mgf
+*.idXML
+*.consensusXML
+*.featureXML
+*.mzid
+*.mzData
+*.dta
+*.dta2d
+
+# DNA/RNA alignment file
+*.sam
+*.bam
+*.bai
+*.cram
+*.crai
+
+# Variant file
+*.bcf
+*.csi
+*.vcf
+*.tbi
+*.maf
+*.idx
+
+# Compressed file
+*.gz
+*.tar
+*.zip
+*.bz2
+
+# Image file
+*.jpeg
+*.jpg
+*.png
+*.tif
+*.tiff
+*.gif
+
+# Document file
+*.pdf
+*.rtf
+*.doc
+*.docx
+*.xls
+*.xlsx
+*.ppt
+*.pptx
+
+# Temporary file
+*.tmp
+*.temp
+*.xlk
+*.~vsd*

CHANGELOG.md

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+# Changelog
+All notable changes to the tool-create-release Action.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
+
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+---
+
+## Unreleased
+
+### Added
+
+- Initial commit