Adding base project scaffold inherited from OpenOmics/nanite

.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 = 4

.gitattributes

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+*.smk linguist-language=Python
+Snakefile linguist-language=Python

.github/workflows/docs.yml

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+name: docs
+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

.github/workflows/main.yaml

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+name: tests
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+      - main
+  pull_request:
+    branches_ignore: []
+
+jobs:
+  Dry_Run_and_Lint:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: docker://snakemake/snakemake:v5.24.2
+    - name: Dry Run with test data
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 \
+        /opt2/mpox-seek run --input \
+        /opt2/.tests/WT_S1_0.fastq.gz /opt2/.tests/WT_S1_1.fastq.gz \
+        /opt2/.tests/WT_S2_0.fastq.gz /opt2/.tests/WT_S2_1.fastq.gz \
+        /opt2/.tests/WT_S3_1.fastq.gz /opt2/.tests/WT_S3_2.fastq.gz \
+        /opt2/.tests/WT_S3_3.fastq.gz /opt2/.tests/WT_S3_4.fastq.gz \
+        /opt2/.tests/WT_S4.fastq.gz /opt2/.tests/WT_S5.fastq.gz \
+        --output /opt2/output --mode local --dry-run
+    - name: View the pipeline config file
+      run: |
+        echo "Generated config file for pipeline...." && cat $PWD/output/config.json
+    - name: Lint Workflow
+      continue-on-error: true
+      run: |
+        docker run -v $PWD:/opt2 snakemake/snakemake:v5.24.2 snakemake --lint -s /opt2/output/workflow/Snakefile -d /opt2/output || \
+        echo 'There may have been a few warnings or errors. Please read through the log to determine if its harmless.'

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+site/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# DS_Store
+.DS_Store
+._*
+**/.DS_Store
+**/._*
+
+.snakemake*
+**/.snakemake*
+.venv
+.venv/*
+
+# Pipeline Results or Output
+results/
+output/
+tmp/
+scratch/
+
+# mkdocs documentation
+site/
+
+# Pipeline generated files or directories
+.tests/*/
+.snakemake/
+
+# Cached Java directories
+.oracle_jre_usage/
+.java/
+
+# GNU Parallel
+.parallel/
+
+# Temp files
+*.tmp
+**/*.tmp
+
+# Test script and test 
+# output directories
+test.sh
+test_*/
+tmp_*/

CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.1.0-beta] - 2024-03-29
+### Start
+  - Created scaffold from [nanite](https://github.com/OpenOmics/nanite) for building the pipeline

LICENSE

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+MIT License
+
+Copyright (c) 2024 OpenOmics
+
+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.

VERSION

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+0.1.0

config/cluster.json

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+{
+    "__default__": {
+        "threads": "2",
+        "mem": "8g",
+        "partition": "norm",
+        "gres": "lscratch:32",
+        "time": "0-04:00:00"
+    }
+}

config/config.json

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+{
+    "options": {
+    }
+}

config/containers.json

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+{
+    "images": {
+        "mpox-seek": "docker://skchronicles/mpox:v0.1.0"
+    }
+}

config/genome.json

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+{
+    "references": {
+
+    }
+}

config/install.json

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+{
+    "install": {
+        "resource_bundle": {
+
+        }
+    }
+}

config/modules.json

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+{
+    "modules": {
+    },
+    "conda":{
+        "mpox-seek": "workflow/envs/mpox.yaml"
+    }
+}

docker/README.md

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+## Steps for Building Docker Images
+
+Directly below are instructions for building an image using the provided Dockerfile:
+
+```bash
+# See listing of images on computer
+docker image ls
+
+# Build from Dockerfile
+docker build --no-cache -f example.dockerfile --tag=example:v0.1.0 .
+
+# Testing, take a peek inside
+docker run -ti example:v0.1.0 /bin/bash
+
+# Updating Tag  before pushing to DockerHub
+docker tag example:v0.1.0 skchronicles/example:v0.1.0
+docker tag example:v0.1.0 skchronicles/example         # latest
+
+# Check out new tag(s)
+docker image ls
+
+# Push new tagged image to DockerHub
+docker push skchronicles/example:v0.1.0
+docker push skchronicles/example:latest
+```
+
+### Other Recommended Steps
+
+Scan your image for known vulnerabilities:
+
+```bash
+docker scan example:v0.1.0
+```
+
+> **Please Note**: Any references to `skchronicles` should be replaced your username if you would also like to push the image to a non-org account.