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Diff for: ‎.github/workflows/conventional-prs.yml

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

Diff for: ‎.github/workflows/main.yml

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

Diff for: ‎.github/workflows/release-please.yml

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on:
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push:
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branches:
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- main
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name: release-please
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jobs:
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release-please:
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runs-on: ubuntu-latest
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steps:
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- uses: GoogleCloudPlatform/release-please-action@v2
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id: release
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with:
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release-type: go # just keep a changelog, no version anywhere outside of git tags
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package-name: <repo>

Diff for: ‎.gitignore

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

Diff for: ‎.snakemake-workflow-catalog.yml

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# configuration of display in snakemake workflow catalog: https://snakemake.github.io/snakemake-workflow-catalog
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usage:
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mandatory-flags: # optional definition of additional flags
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desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
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flags: # put your flags here
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software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
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conda: true # whether pipeline works with --use-conda
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singularity: false # whether pipeline works with --use-singularity
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singularity+conda: false # whether pipeline works with --use-singularity --use-conda
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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

Diff for: ‎.template/config/config.yaml.tmpl.tmpl

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

Diff for: ‎.template/workflow/Snakefile.tmpl.tmpl

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

Diff for: ‎LICENSE

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MIT License
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Copyright (c) 2021, AUTHORS
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

Diff for: ‎README.md

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# Snakemake workflow: `<name>`
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[![Snakemake](https://img.shields.io/badge/snakemake-≥6.3.0-brightgreen.svg)](https://snakemake.github.io)
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[![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)
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A Snakemake workflow for `<description>`
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## Usage
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The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=<owner>%2F<repo>).
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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).
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# TODO
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* Replace `<owner>` and `<repo>` everywhere in the template (also under .github/workflows) with the correct `<repo>` name and owning user or organization.
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* Replace `<name>` with the workflow name (can be the same as `<repo>`).
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* Replace `<description>` with a description of what the workflow does.
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* 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.

Diff for: ‎config/README.md

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

Diff for: ‎workflow/Snakefile

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# Main entrypoint of the workflow.
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# Please follow the best practices:
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# https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html,
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# in particular regarding the standardized folder structure mentioned there.

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