Initial commit

.github/PULL_REQUEST_TEMPLATE.md

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+## Description
+
+<!--- Briefly describe the changes included in this pull request
+ !--- starting with 'Closes #...' if approriate --->
+
+Closes #...
+
+## Checklist 
+
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
+
+### Formatting
+
+- [ ] I have read the [code review guidelines](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Guidelines) and the [code review best practice on GitHub check-list](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/Code+Review+Best+Practice+on+GitHub+-+Check+List).
+
+- [ ] The name of the branch is meaningful and well formatted following the [standards](https://confluence.mednet.ucla.edu/display/BOUTROSLAB/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 set up or verified the branch protection rule following the [github standards](https://confluence.mednet.ucla.edu/pages/viewpage.action?spaceKey=BOUTROSLAB&title=GitHub+Standards#GitHubStandards-Branchprotectionrule) before opening this pull request.
+
+### File Updates
+
+- [ ] I have ensured that the version number update follows the [semantic versioning standards](http://semver.org/).
+
+- [ ] I have updated the version number/requirements and added my name to the author list in the `setup.cfg`.
+
+- [ ] I have updated the version number/feature changes in the `README.md`.
+
+<!--- This acknowledgement is optional if you do not want to be listed--->
+- [ ] I have updated the version number and added my name to the contributors list in the `metadata.yaml`.
+
+- [ ] I have added the changes included in this pull request to the `CHANGELOG.md` under the next release version or unreleased, and updated the date.
+
+<!---If any previous versions have bugs, add "deprecated" in the version tag and list the bug in the corresponding release--->
+- [ ] I have drafted the new version release with any additions/changes and have linked the `CHANGELOG.md` in the release. 
+
+### Testing
+
+- [ ] I have added unit tests for the new feature(s).
+
+- [ ] I modified the integration test(s) to include the new feature.
+
+- [ ] All existing tests for [this tool] passed locally and/or on the cluster.

.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://blcdsdockerregistry/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
+
+# Compressed file
+*.gz
+*.tar
+*.zip

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
+- Changed something but it is not part of the last release.
+
+---
+
+## [1.0.0] - YYYY-MM-DD
+### Added
+- For new features.
+- Added item 1.
+
+### Changed
+- For changes in existing functionality.
+- Changed item 1.
+
+### Deprecated
+- For soon-to-be removed features.
+
+### Removed
+- For now removed features.
+- Removed item 1.
+
+### Fixed
+- For any bug fixes.
+- Fixed item 1.
+
+### Security
+- In case of vulnerabilities.