Initial commit

.gitattributes

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+*.config linguist-language=groovy

.github/CODEOWNERS

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+# Default owner(s)
+*	@tyamaguchi-ucla @yashpatel6 @zhuchcn @uclahs-cds/software-wg

.github/ISSUE_TEMPLATE/issue_report.md

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+---
+name: Issue report
+about: Create a report to help us improve our pipelines
+title: "[ISSUE]: "
+labels: ''
+assignees: ''
+
+---
+
+**Describe the issue**<br>
+A clear and concise description of what the issue is. Please include the following in your issue report along with any explicit errors observed
+
+**Error:**
+```
+paste relevant error message here, if applicable
+```
+
+**Screenshots**<br>
+If applicable, add screenshots to help explain your problem.
+
+---
+
+**Pipeline release version:**<br>
+`version`
+
+**Cluster you are using:**
+- [ ] `Slurm-Dev`
+- [ ] `Slurm-Test`
+- [ ] `Regeneron`
+
+**Node type:**
+<!-- specify another scratch size here if it's not the default. eg.) 3TB for F72+3TB  --->
+- [ ] `F2`   &numsp;&emsp;  (scratch: `32GB`)
+- [ ] `F16`         &emsp;  (scratch: `500GB`)
+- [ ] `F32`         &emsp;  (scratch: `500GB`)
+- [ ] `F72`         &emsp;  (scratch: `2TB`)
+- [ ] `M64`         &emsp;  (scratch: `2TB`)
+
+**Submission method**
+- [ ] interactive
+- [ ] submission script
+
+**Actual submission command**<br>
+Paste the command used inside your script if you used one.
+<!-- 
+EXAMPLE:
+    - `python3 /path/to/submit_nextflow_pipeline.py --nextflow_script ...`
+    - `nextflow run ...`
+    - etc...
+--->
+
+```
+submission command
+```
+
+**Paths**
+<!-- Please enter the paths under the table below --->
+
+| Description | Path |
+|-------------|------|
+| sbatch/qsub command and logs <br> (if applicable) | ```/path/to/logs```|
+| Config File                                       | ```/path/to/config/file``` |
+| Working Directory                                 | ```/path/to/work/dir``` |
+| Logs Produceded by the Pipeline                   | ```/path/to/logs``` |
+
+
+---
+
+**To Reproduce**<br>
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**<br>
+A clear and concise description of what you expected to happen.
+
+**Additional context**<br>
+Add any other context about the problem here.

.github/PULL_REQUEST_TEMPLATE.md

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+> This is a template for UCLA-CDS pipeline developers to create a github pull request template. Things should be adjusted for individual pipeline including:
+> 1. additional checklist items sepecific to the pipeline
+> 2. a description of how testing is expected to be done
+> 3. a template list or table for testing results
+> 4. additional notes wrapped in \<!--- ---> (or \<!-- --\> for inline comments) that help PR submitters to fill in.
+> 5. delete this block of instructional text.
+
+# Description
+<!--- Briefly describe the changes included in this pull request and the paths to the test cases below
+ !--- starting with 'Closes #...' if appropriate --->
+
+### Closes #...
+
+## Testing 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 -->
+- 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 -->
+- NFTest
+    - output:    <!-- path/to/output -->
+    - log:       <!-- path/to/log -->
+    - cases:     <!-- list of test cases run -->
+
+# Checklist
+<!--- Please read each of the following items and confirm by replacing the [ ] with a [X] --->
+
+- [ ] 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 reviewed the [Nextflow pipeline standards](https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3193890/Nextflow+pipeline+standardization).
+
+- [ ] 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 set up or verified the 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.
+
+- [ ] I have added my name to the contributors listings in the ``manifest`` block in the `nextflow.config` as part of this pull request, am listed
+already, or do not wish to be listed. (*This acknowledgement is optional.*)
+
+- [ ] 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.
+
+- [ ] I have updated the version number in the `metadata.yaml` and `manifest` block of the `nextflow.config` file following [semver](https://semver.org/), or the version number has already been updated. (*Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.*)
+
+- [ ] I have tested the pipeline on at least one A-mini sample.

.github/dependabot.yml

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+---
+version: 2
+updates:
+  - package-ecosystem: "gitsubmodule"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      # Group these two modules together for pull requests
+      # "pipeline-submodules" is an arbitrary name
+      pipeline-submodules:
+        patterns:
+          - "*/pipeline-Nextflow-config"
+          - "*/pipeline-Nextflow-module"

.github/workflows/deploy-docs.yaml

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+---
+name: Build and Deploy Docs
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    tags:
+      - 'v[0-9]*'
+
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout main
+        uses: actions/checkout@v4
+
+      - name: Deploy docs
+        uses: uclahs-cds/tool-Nextflow-action/build-and-deploy-docs@main

.github/workflows/nextflow-tests.yaml

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+---
+name: Nextflow config tests
+
+on:
+  workflow_run:
+    workflows: [Trigger Tests]
+    types:
+      - completed
+
+permissions:
+  actions: read
+  contents: write
+  packages: read
+  pull-requests: write
+  statuses: write
+
+jobs:
+  tests:
+    if: ${{ github.event.workflow_run.conclusion == 'success' }}
+    uses: uclahs-cds/tool-Nextflow-action/.github/workflows/nextflow-tests.yml@main
+    secrets: inherit

.github/workflows/pipeline-release.yaml

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+---
+on:
+  push:
+    tags: "v*"
+  release:
+    types: [published]
+
+permissions: read-all
+jobs:
+  add_release_asset:
+    runs-on: ubuntu-latest
+    name: A job to add a release asset with submodules
+    steps:
+      - id: release-asset
+        uses: uclahs-cds/tool-Nextflow-action/add-source-with-submodules@latest
+        with:
+          my-token: ${{ secrets.UCLAHS_CDS_REPO_READ_TOKEN }}

.github/workflows/render-puml.yaml

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+---
+name: PlantUML Generation
+
+on:
+  push:
+    paths:
+      - '**.puml'
+  workflow_dispatch:
+
+jobs:
+  plantuml:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Generate PUML diagrams
+        uses: uclahs-cds/[email protected]
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          ghcr-username: ${{ github.actor }}
+          ghcr-password: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/static-analysis.yml

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

.github/workflows/trigger-tests.yaml

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+---
+name: Trigger tests
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_target:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+
+permissions:
+  pull-requests: write
+  statuses: write
+
+jobs:
+  check-user:
+    uses: uclahs-cds/tool-Nextflow-action/.github/workflows/test-setup.yml@main

.gitignore

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+# System files
+*.log
+*.error
+.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

.gitmodules

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+[submodule "external/pipeline-Nextflow-module"]
+	path = external/pipeline-Nextflow-module
+	url = [email protected]:uclahs-cds/pipeline-Nextflow-module.git
+[submodule "external/pipeline-Nextflow-config"]
+	path = external/pipeline-Nextflow-config
+	url = [email protected]:uclahs-cds/pipeline-Nextflow-config.git