Initial commit

.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 -->
+
+<!-- 
+Admin/maintainer: please edit the 'Pipeline Run Results' or 'Analysis Results' sections as needed for your project repo.  
+Then commit/push the changes so everyone uses this template for future PRs.
+
+For example, if your project is a `pipeline`, then create a 'Pipeline Run Results' section.
+
+If your project is a general data analysis project, then you may want to require an 'Analysis Results' section in order to test
+code from each PR to help prevent creating new bugs.
+-->
+
+## Pipeline Run Results
+
+- Case 1
+    - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
+    - input csv: <!-- path/to/input.csv -->
+    - config:    <!-- path/to/xxx.config -->
+    - output:    <!-- path/to/output -->
+    - log:       <!-- path/to/log -->
+- Case 2
+    - sample:    <!-- e.g. A-mini S2.T-1, A-mini S2.T-n1 -->
+    - input csv: <!-- path/to/input.csv -->
+    - config:    <!-- path/to/xxx.config -->
+    - output:    <!-- path/to/output -->
+    - log:       <!-- path/to/log -->
+
+## Analysis Results
+
+- Case 1
+    - script:    <!-- path/to/script.R -->
+    - command:   <!-- path/to/launch.sh -->
+    - output:    <!-- path/to/output -->
+- Case 2
+    - script:    <!-- path/to/script.R -->
+    - command:   <!-- path/to/launch.sh -->
+    - output:    <!-- path/to/output -->
+
+# 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/CICD-base.yaml

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+---
+name: CICD-base
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+jobs:
+  CICD-base:
+    runs-on: ubuntu-latest
+
+    timeout-minutes: 15
+
+    steps:
+      # Checkout codebase
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      # Run CICD-base
+      - name: CICD-base
+        uses: docker://ghcr.io/uclahs-cds/cicd-base:latest

.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_name Docker file.
+
+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]
+### Changed
+- Update links in on-prem Confluence to point to cloud-based Confluence
+- Update `.gitignore` - Add common non-plain text file extensions (e.g. image and Office suite)
+- Change something but it is not part of the last release.
+
+---
+
+## [1.0.0] - YYYY-MM-DD
+### Added
+- For new features.
+- Add item 1.
+
+### Changed
+- For changes in existing functionality.
+- Change item 1.
+
+### Deprecated
+- For soon-to-be removed features.
+
+### Removed
+- For now removed features.
+- Remove item 1.
+
+### Fixed
+- For any bug fixes.
+- Fix item 1.
+
+### Security
+- In case of vulnerabilities.