Initial commit

.editorconfig

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+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+
+[*.{yml,yaml}]
+indent_style = space
+indent_size = 2

.gitattributes

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+*.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior; if applicable, add screenshots to help explain your problem:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.

.github/ISSUE_TEMPLATE/enchancement_request.md

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+---
+name: Enhancement request
+about: Suggest an additional component to an already existing feature
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Describe what enhancement you'd like to see.**
+A clear and concise description of what you'd like to add, specifically to what already existing feature. Ex. I am using a new reference, and I'd love to see this reference included [...]
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen. If there are alternative solutions or features you've considered, please include these!

.github/PULL_REQUEST_TEMPLATE/pull_request_template.md

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+---
+
+name: Pull Request report
+about: Create a Pull Request for the pipeline
+title: ''
+labels: ''
+assignees: ''
+
+**Overview of the Request**
+Provide a summary of what is included in this Pull Request
+
+**Issues**
+Reference any issues that were included in this request.
+
+**Reviewers**
+Use the @ feature to mention anyone responsible for reviewing/completing this request.
+
+## Checklist
+
+(~Strikethrough~ any points that are not applicable.)
+
+- [ ] Write unit tests for any new features or bug fixes.
+- [ ] Update docs if there are any API changes.
+- [ ] Update the changelog if this includes any user-facing changes.

.github/workflows/build_mkdocs.yml

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+name: mkdocs_build
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - "docs/**"
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+      - run: pip install --upgrade pip
+      - run: pip install -r docs/requirements.txt
+      - run: mkdocs gh-deploy --force

.gitignore

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+# Compiled class file
+*.class
+
+# Log file
+*.log
+
+# BlueJ files
+*.ctxt
+
+# Mobile Tools for Java (J2ME)
+.mtj.tmp/
+
+# Package Files #
+*.jar
+*.war
+*.nar
+*.ear
+*.zip
+*.tar.gz
+*.rar
+
+# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
+hs_err_pid*
+replay_pid*
+
+# nextflow
+.nextflow*
+work/
+data/
+results/
+/nextflow.config
+/params.yaml
+
+# python packaging
+*.pyc
+*.egg-info
+
+# macOS
+.DS_Store

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v1.2.3
+    hooks:
+      - id: check-added-large-files
+      #- id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+  # Python formatting
+  - repo: https://github.com/psf/black
+    rev: 23.7.0
+    hooks:
+      - id: black
+  # R formatting
+  - repo: https://github.com/lorenzwalthert/precommit
+    rev: v0.1.2
+    hooks:
+      - id: style-files
+  # general linting
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

.prettierrc

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+overrides:
+    - files: "*.md"
+      options:
+          tabWidth: 2

LICENSE

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+MIT License
+
+Copyright (c) 2023, CCR Collaborative Bioinformatics Resource
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

MANIFEST.in

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+include LICENSE
+recursive-include src *

README.md

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+# Nextflow Template
+
+CCBR template for creating Nextflow pipelines
+
+This template takes inspiration from nektool[^1] and the nf-core template. If you plan to contribute your pipeline to nf-core, don't use this template -- instead follow their instructions[^2].
+
+[^1]: nektool https://github.com/beardymcjohnface/nektool
+[^2]: instructions for nf-core pipelines https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core
+
+## Getting started
+
+1. Create a new repository from this template using either of these options:
+   - [**The GitHub web interface**](https://github.com/CCBR/CCBR_NextflowTemplate):
+     Click "Use this template" and "Create a new repository", then choose an owner (CCBR) and the repository name as the new tool's name.
+   - [**The GitHub command line interface**](https://cli.github.com/):
+     ```sh
+     gh repo create CCBR/TOOL_NAME \
+        --description "One-line description of your tool" \
+        --public \
+        --template CCBR/CCBR_NextflowTemplate \
+        --confirm
+     ```
+1. Change all instances of `TOOL_NAME` throughout the repo with the actual tool name. Places include:
+   - `docs/CHANGELOG.md`
+   - `mkdocs.yml`
+   - `README.md`
+   - `pyproject.toml`
+   - `src/TOOL_NAME`
+   - `src/TOOL_NAME/CITATION`
+   - `src/TOOL_NAME/__main__.py`
+1. Edit `pyproject.toml` with correct information for your tool. You will likely need to change:
+   - author names and emails
+   - dependencies
+   - project URLs
+1. Write your nextflow workflow in `src/TOOL_NAME/workflow`.
+1. Write your documentation in `docs/` and enable GitHub Pages.
+   - In settings, go to General > Pages and select the `gh-pages` branch.
+     mkdocs will build your site under the `gh-pages` branch, and GitHub Pages will make it available at `https://ccbr.github.io/TOOL_NAME`.
+
+You can look for instances of `TOOL_NAME` in case you missed any with grep:
+
+```sh
+grep -r "TOOL_NAME" *
+```
+
+## Usage
+
+Install the tool in edit mode:
+
+```sh
+pip3 install -e .
+```
+
+Run the example
+
+```sh
+TOOL_NAME run --input "Hello world"
+```
+
+## Maintaining your tool
+
+### Use pre-commit hooks
+
+Pre-commit can automatically format your code, check for spelling errors, etc. every time you commit.
+
+Install [pre-commit](https://pre-commit.com/#installation) if you haven't already,
+then run `pre-commit install` to install the hooks specified in `.pre-commit-config.yaml`.
+Pre-commit will run the hooks every time you commit.
+
+### Versions
+
+Increment the version number following semantic versioning[^3] in `src/TOOL_NAME/VERSION`
+
+[^3]: semantic versioning guidelines https://semver.org/
+
+### Changelog
+
+Keep the changelog up to date with any user-facing changes in `docs/CHANGELOG.md`

docs/CHANGELOG.md

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+## TOOL_NAME v0.1.0.apha
+
+### API-breaking changes
+
+- change 1
+- example 2
+
+### New features
+
+- new feat 1
+
+### Bug fixes
+
+- description of bug fixed
+
+## TOOL_NAME v0.1.0
+
+This is the first release of TOOL_NAME 🎉

docs/index.md

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+Information on who the pipeline was developed for, and a statement if it's only been tested on Biowulf. For example:
+
+It has been developed and tested solely on NIH [HPC Biowulf](https://hpc.nih.gov/).
+
+Also include a workflow image to summarize the pipeline.

docs/requirements.txt

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+#https://pypi.org/project/mkdocs-git-revision-date-localized-plugin/
+mkdocs-git-revision-date-localized-plugin==1.2.0
+#https://pypi.org/project/mkdocs-minify-plugin/
+mkdocs-minify-plugin==0.6.4
+#https://pypi.org/project/mkdocs-git-revision-date-plugin/
+mkdocs-git-revision-date-plugin==0.3.2
+#https://pypi.org/project/mkdocs-material/
+mkdocs-material==9.1.6
+#https://pypi.org/project/mkdocs-material-extensions/
+mkdocs-material-extensions==1.1.1

docs/user-guide/contributions.md

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+Should include a list of all contributors, including GitHub handles when appropriate. In addition, a statement of who contributed to the source code specifically, identified by initials. An example is included below.
+
+# Contributions
+
+The following members contributed to the development of the CARLISLE pipeline:
+
+- [Samantha Sevilla](https://github.com/slsevilla)
+
+SS contributed to the generating the source code and all members contributed to the main concepts and analysis.

docs/user-guide/getting-started.md

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+This should set the stage for all of the pipeline requirements. Examples are listed below.
+
+# Overview
+
+The CARLISLE github repository is stored locally, and will be used for project deployment. Multiple projects can be deployed from this one point simultaneously, without concern.
+
+## 1. Getting Started
+
+## 1.1 Introduction
+
+The CARLISLE Pipelie beings with raw FASTQ files and performs trimming followed by alignment using [BOWTIE2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Data is then normalized through either the use of an user-species species (IE E.Coli) spike-in control or through the determined library size. Peaks are then called using [MACS2](https://hbctraining.github.io/Intro-to-ChIPseq/lessons/05_peak_calling_macs.html), [SEACR](https://github.com/FredHutch/SEACR), and [GoPEAKS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02707-w) with various options selected by the user. Peaks are then annotated, and summarized into reports. If designated, differential analysis is performed using [DESEQ2](https://bioconductor.org/packages/release/bioc/html/DESeq2.html). QC reports are also generated with each project using [FASTQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [MULTIQC](https://multiqc.info/). Annotations are added using [HOMER](http://homer.ucsd.edu/homer/ngs/annotation.html) and [ROSE](https://github.com/stjude/ROSE). GSEA Enrichment analysis predictions are added using [CHIPENRICH](https://bioconductor.org/packages/devel/bioc/vignettes/chipenrich/inst/doc/chipenrich-vignette.html).
+
+The following are sub-commands used within CARLISLE:
+
+- initialize: initialize the pipeline
+- dryrun: predict the binding of peptides to any MHC molecule
+- cluster: execute the pipeline on the Biowulf HPC
+- local: execute a local, interactive, session
+- git: execute GitHub actions
+- unlock: unlock directory
+- DAG: create DAG report
+- report: create SNAKEMAKE report
+- testrun: copies test manifests and files to WORKDIR
+
+## 1.2 Setup Dependencies
+
+CARLISLE has several dependencies listed below. These dependencies can be installed by a sysadmin. All dependencies will be automatically loaded if running from Biowulf.
+
+- bedtools: "bedtools/2.30.0"
+- bedops: "bedops/2.4.40"
+
+## 1.3 Login to the cluster
+
+CARLISLE has been exclusively tested on Biowulf HPC. Login to the cluster's head node and move into the pipeline location.
+
+```
+# ssh into cluster's head node
+ssh -Y [email protected]
+```
+
+## 1.4 Load an interactive session
+
+An interactive session should be started before performing any of the pipeline sub-commands, even if the pipeline is to be executed on the cluster.
+
+```
+# Grab an interactive node
+sinteractive --time=12:00:00 --mem=8gb  --cpus-per-task=4 --pty bash
+```