A Snakemake workflow for processing PROseq data. It is an add-on to my fastq-process-align workflow. This workflow will perform the following:

1. Preprocess FASTQ files, including adapter trimming, quality trimming/filtering, and UMI extraction
2. Align to the genome using standard tools (bowtie2, star, bwa, and minimap)
3. Deduplicate mapped reads
4. Identify transcription start regions

• Snakemake workflow: <name>
  • Usage
  • Deployment options
  • Authors
  • References
  • TODO

The usage of this workflow is described in the Snakemake Workflow Catalog.

Detailed information about input data and workflow configuration can also be found in the config/README.md.

If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.

To run the workflow from command line, change the working directory.

cd path/to/snakemake-workflow-name

Adjust options in the default config file config/config.yaml. Before running the complete workflow, you can perform a dry run using:

snakemake --dry-run

To run the workflow with test files using conda:

snakemake --cores 2 --sdm conda --directory .test

To run the workflow with apptainer / singularity, add a link to a container registry in the Snakefile, for example container: "oras://ghcr.io/<user>/<repository>:<version>" for Github's container registry. Run the workflow with:

snakemake --cores 2 --sdm conda apptainer --directory .test

• Arya Zandvakili
  • 0000-0001-8031-8067

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.

• Replace <owner> and <repo> everywhere in the template with the correct user name/organization, and the repository name. The workflow will be automatically added to the snakemake workflow catalog once it is publicly available on Github.
• Replace <name> with the workflow name (can be the same as <repo>).
• Replace <description> with a description of what the workflow does.
• Update the deployment, authors and references sections.
• Update the README.md badges. Add or remove badges for conda/singularity/apptainer usage depending on the workflow's deployment options.
• Do not forget to also adjust the configuration-specific config/README.md file.