Snakemake workflow catalog

Standardized usage
All workflows

	Workflow	Description	Topics	QC	Stars	Watchers

Description	Topics	QC	Stars	Watchers

Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it can be installed via Mambaforge. For other options see here.

Given that Mamba is installed, run

mamba create -c bioconda -c conda-forge --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

Given that Snakemake and Snakedeploy are installed and available (see Step 1), the workflow can be deployed as follows.

First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory.

Second, run

Snakedeploy will create two folders workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs. Later, when executing the workflow, Snakemake will automatically find the main Snakefile in the workflow subfolder.

Third, consider to put this directory under version control, e.g. by managing it via a (private) Github repository

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser via

snakemake --report report.zip

The resulting report.zip file can be passed on to collaborators, provided as a supplementary file in publications, or uploaded to a service like Zenodo in order to obtain a citable DOI.

All workflows

This catalog includes workflows based on the following criteria:

The workflow is contained in a public Github repository.
The repository has a readme, containing the words "snakemake" and "workflow" (case insensitive).
The repository contains a workflow definition named either Snakefile or workflow/Snakefile.
If the repository contains a folder rules or workflow/rules that folder must at least contain one file ending on .smk.
The repository is small enough to be cloned into a Github actions job (very large files should be handled via Git LFS, so that they can be stripped out during cloning).
The repository is not blacklisted here.

Standardized usage

In order to additionally appear in the "standardized usage" area, repositories additionally have to

have their main workflow definition named workflow/Snakefile (unlike for plain inclusion (see above), which also allows just Snakefile in the root of the repository),
provide configuration instructions under config/README.md,

contain a YAML file .snakemake-workflow-catalog.yml in their root directory, which configures the usage instructions displayed by this 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: true # whether pipeline works with --use-singularity
    singularity+conda: true # 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

Once included in the standardized usage area you can link directly to the usage instructions for your repository via the URL https://varlociraptor.github.io/snakemake-workflow-catalog?usage=<owner>/<repo>.

Release handling

If your workflow provides Github releases, we will always just scrape the latest non-preview release. Hence, in order to update your workflow's records here, you need to release a new version on Github.