Rewrite of workflow template with most recent best practices.

.github/workflows/conventional-prs.yml

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+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

.github/workflows/main.yml

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+name: Tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Formatting
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: master
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Lint workflow
+      uses: snakemake/[email protected]
+      with:
+        directory: .
+        snakefile: workflow/Snakefile
+        args: "--lint"
+
+  Testing:
+    runs-on: ubuntu-latest
+    needs: 
+      - Linting
+      - Formatting
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Test workflow
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"
+
+    - name: Test report
+      uses: snakemake/[email protected]
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--report report.zip"

.github/workflows/release-please.yml

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+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+
+      - uses: GoogleCloudPlatform/release-please-action@v2
+        id: release
+        with:
+          release-type: python
+          package-name: snakemake
+
+      - uses: actions/checkout@v2
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.x'
+
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          python -m pip install --upgrade pip
+          python setup.py sdist
+
+      - name: Publish to PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+
+      - name: Publish to Registry
+        if: ${{ steps.release.outputs.release_created }}
+        uses: elgohr/[email protected]
+        with:
+          name: snakemake/snakemake
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+          tags: "v${{ steps.release.outputs.major }}.${{ steps.release.outputs.minor }}.${{ steps.release.outputs.patch }},stable"

.gitignore

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+results/**
+resources/**
+.snakemake
+.snakemake/**

.snakemake-workflow-catalog.yml

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+usage:
+  software-stack-deployment:
+    conda: true
+  report: true

LICENSE

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+MIT License
+
+Copyright (c) 2019, Felix Mölder, Johannes Köster
+
+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.

README.md

@@ -1,28 +1,15 @@
-# A best practice template for Snakemake workflows
+# Snakemake workflow: dna-seq-varlociraptor
 
-To generate a new structure using this template, run
+[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)
+[![GitHub actions status](https://github.com/snakemake-workflows/dna-seq-varlociraptor/workflows/Tests/badge.svg?branch=main)](https://github.com/snakemake-workflows/dna-seq-varlociraptor/actions?query=branch%3Amain+workflow%3ATests)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4675661.svg)](https://doi.org/10.5281/zenodo.4675661)
 
-    copier gh:snakemake-workflows/snakemake-workflow-template <path>
 
-with path pointing to the desired output directory.
+A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of [Varlociraptor](https://varlociraptor.github.io).
 
-You will get the following structure:
 
-    ├── copier.yml
-    ├── README.md
-    ├── .template
-    │   ├── config
-    │   │   └── config.yaml.tmpl
-    │   └── workflow
-    │       └── Snakefile.tmpl
-    └── workflow
-        ├── rules
-        │   └── common.smk
-        └── Snakefile
+## Usage
 
-The `workflow` folder contains the structure to put the actual workflow in.
-Make sure to follow the [best practices](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#distribution-and-reproducibility).
+The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows%2Fdna-seq-varlociraptor).
 
-The `.template` folder contains an automatically generated template for deploying the workflow using Snakemake's [module system](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#snakefiles-modules).
-Here, you should edit the `config.yaml.tmpl` to contain the config settings you would like to initialize in the deployment of the user.
-It is possible to add further files needed for the configuration to the `.template` folder, e.g. sample sheets.
+If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above).

config/README.md

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+Describe how to configure the workflow (using config.yaml and maybe additional files).
+All of them need to be present with example entries inside of the config folder.

workflow/Snakefile

@@ -1,12 +1,4 @@
-# The main entry point of your workflow.
-# After configuring, running snakemake -n in a clone of this repository should successfully execute a dry-run of the workflow.
-
-
-rule all:
-    input:
-        # The first rule should define the default target files
-        # Subsequent target rules can be specified below. They should start with all_*.
-
-
-# use includes for common helper functions and sets of rules that serve a common theme
-include: "rules/common.smk"
+# Main entrypoint of the workflow. 
+# Please follow the best practices: 
+# https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html,
+# in particular regarding the standardized folder structure mentioned there.