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init snakemake workflow project
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‎.github/workflows/conventional-prs.yml‎

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name: Lint 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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permissions:
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pull-requests: read
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jobs:
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main:
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name: Validate PR title
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runs-on: ubuntu-latest
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steps:
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- uses: amannn/action-semantic-pull-request@v5
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/deploy_apptainer.yml‎

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name: Deploy Apptainer
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on:
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workflow_run:
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workflows: ["release-please"]
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types:
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- completed
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workflow_dispatch:
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jobs:
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build_and_push:
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
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steps:
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- name: checkout repo
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: add apptainer source
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shell: bash
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run: |
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sudo add-apt-repository -y ppa:apptainer/ppa
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sudo apt-get update
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- name: create dockerfile
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uses: snakemake/snakemake-github-action@v2
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with:
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directory: .
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snakefile: workflow/Snakefile
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install-apptainer: true
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args: "--cores 1"
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task: containerize
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- name: create apptainer recipe
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shell: bash
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run: |
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pip install spython
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sed -i "2i RUN apt-get update && apt-get install -y curl" Dockerfile
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spython recipe Dockerfile > apptainer.def
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sed -i 's/\/environment.yaml\/environment.yaml$/\/environment.yaml/' apptainer.def
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- name: create apptainer image
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shell: bash
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run: |
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sudo apt-get install -y uidmap
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apptainer build --fakeroot apptainer.sif apptainer.def
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- name: authenticate to GHCR
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run: |
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echo ${{ secrets.GITHUB_TOKEN }} | apptainer registry login -u ${{ github.actor }} --password-stdin oras://ghcr.io
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- name: push apptainer to GHCR
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run: |
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REPO=$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')
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echo "Pushing apptainer to: oras://ghcr.io/${REPO}:latest"
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apptainer push apptainer.sif "oras://ghcr.io/${REPO}:latest"

‎.github/workflows/main.yml‎

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name: CI
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on:
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push:
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branches: [main, dev]
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pull_request:
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branches: [main, dev]
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jobs:
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Formatting:
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runs-on: ubuntu-latest
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if: ${{ github.actor != 'github-actions[bot]' }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Test formatting
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uses: super-linter/super-linter@v7
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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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VALIDATE_YAML_PRETTIER: true
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Linting:
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runs-on: ubuntu-latest
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if: ${{ github.actor != 'github-actions[bot]' }}
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steps:
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- uses: actions/checkout@v4
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- name: Test linting 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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if: ${{ github.actor != 'github-actions[bot]' }}
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needs:
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- Formatting
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steps:
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- uses: actions/checkout@v4
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- name: Test run 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: "--sdm conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache -n"
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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: "--cores 3 --report report.zip -n"

‎.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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permissions:
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contents: write
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pull-requests: write
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issues: write
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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: googleapis/release-please-action@v4
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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release-type: simple

‎.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/**
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.test/results/*

‎.snakemake-workflow-catalog.yml‎

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usage:
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mandatory-flags:
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desc: # describe your flags here in a few sentences
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flags: # put your flags here
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software-stack-deployment:
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conda: true # whether pipeline works with '--sdm conda'
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apptainer: false # whether pipeline works with '--sdm apptainer/singularity'
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apptainer+conda: true # whether pipeline works with '--sdm conda apptainer/singularity'
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report: true # whether creation of reports using 'snakemake --report report.zip' is supported

‎.test/config/config.yml‎

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samplesheet: "config/samples.tsv"

‎.test/config/samples.tsv‎

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sample,species,strain,id_prefix,file

‎README.md‎

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# snakemake-assembly-postprocessing
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[![Snakemake](https://img.shields.io/badge/snakemake-≥8.24.1-brightgreen.svg)](https://snakemake.github.io)
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[![GitHub actions status](https://github.com/MPUSP/snakemake-assembly-postprocessing/actions/workflows/main.yml/badge.svg)](https://github.com/MPUSP/snakemake-assembly-postprocessing/actions/workflows/main.yml)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with apptainer](https://img.shields.io/badge/run%20with-apptainer-1D355C.svg?labelColor=000000)](https://apptainer.org/)
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A Snakemake workflow for the post-processing of microbial genome assemblies.
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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/docs/workflows/MPUSP/snakemake-assembly-postprocessing).
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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 repository.
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## Authors
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- Dr. Rina Ahmed-Begrich
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- Affiliation: [Max-Planck-Unit for the Science of Pathogens](https://www.mpusp.mpg.de/) (MPUSP), Berlin, Germany
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- ORCID profile: https://orcid.org/0000-0002-0656-1795
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- Dr. Michael Jahn
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- Affiliation: [Max-Planck-Unit for the Science of Pathogens](https://www.mpusp.mpg.de/) (MPUSP), Berlin, Germany
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- ORCID profile: https://orcid.org/0000-0002-3913-153X
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- github page: https://github.com/m-jahn
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## References
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> Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., & Nahnsen, S. _Sustainable data analysis with Snakemake_. F1000Research, 10:33, 10, 33, **2021**. https://doi.org/10.12688/f1000research.29032.2.

‎config/README.md‎

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## Running the workflow
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### Input data
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This workflow requires `fasta` input data.
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The samplesheet table has the following layout:
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| sample | species | strain | id_prefix | file |
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| ----------- | ------------ | ---------------------------------- | ------------- | ------------- |
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| EC2224 | "Streptococcus pyogenes" | SF370 | Spy | assembly.fasta |
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### Execution
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To run the workflow from command line, change to the working directory and activate the conda environment.
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```bash
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cd snakemake-assembly-postprocessing
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conda activate snakemake-assembly-postprocessing
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```
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Adjust options in the default config file `config/config.yml`.
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Before running the entire workflow, perform a dry run using:
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```bash
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snakemake --cores 3 --sdm conda --directory .test --dry-run
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```
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To run the workflow with test files using **conda**:
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```bash
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snakemake --cores 3 --sdm conda --directory .test
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```

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