Initial commit

.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: [ main ]
+  pull_request:
+    branches: [ main ]
+
+
+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: main
+          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: go # just keep a changelog, no version anywhere outside of git tags
+          package-name: <repo>

.gitignore

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

.snakemake-workflow-catalog.yml

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+# configuration of display in snakemake workflow catalog: https://snakemake.github.io/snakemake-workflow-catalog
+
+usage:
+  mandatory-flags: # optional definition of additional flags
+    desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
+    flags: # put your flags here
+  software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
+    conda: true # whether pipeline works with --use-conda
+    singularity: false # whether pipeline works with --use-singularity
+    singularity+conda: false # whether pipeline works with --use-singularity --use-conda
+  report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations

.template/config/config.yaml.tmpl.tmpl

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+# add template configuration file (may use variables from copier.yml)

.template/workflow/Snakefile.tmpl.tmpl

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+configfile: "config/config.yaml"
+
+module [[ module_name ]]:
+    snakefile:
+        # TODO replace <release> with desired release
+        "https://github.com/[[ owner ]]/[[ repo ]]/raw/<release>/Snakefile"
+    config:
+        config
+
+use rule * from [[ module_name ]]

LICENSE

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+MIT License
+
+Copyright (c) 2021, AUTHORS
+
+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

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+# Snakemake workflow: `<name>`
+
+[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)
+[![GitHub actions status](https://github.com/<owner>/<repo>/workflows/Tests/badge.svg?branch=main)](https://github.com/<owner>/<repo>/actions?query=branch%3Amain+workflow%3ATests)
+
+
+A Snakemake workflow for `<description>`
+
+
+## Usage
+
+The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=<owner>%2F<repo>).
+
+If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) <repo>sitory and its DOI (see above).
+
+# TODO
+
+* Replace `<owner>` and `<repo>` everywhere in the template (also under .github/workflows) with the correct `<repo>` name and owning user or organization.
+* Replace `<name>` with the workflow name (can be the same as `<repo>`).
+* Replace `<description>` with a description of what the workflow does.
+* The workflow will occur in the snakemake-workflow-catalog once it has been made public. Then the link under "Usage" will point to the usage instructions if `<owner>` and `<repo>` were correctly set.

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

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+# 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.