This catalog is generated automatically by querying Github APIs; the Snakemake team is not responsible for the linked workflows.
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
to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via
mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy
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:
In all following steps, we will assume that you are inside of that directory.
mkdir -p path/to/project-workdir cd path/to/project-workdir
Snakedeploy will create two folders
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
workflowsubfolder. Third, consider to put this directory under version control, e.g. by managing it via a (private) Github repository
snakemake --report report.zip
report.zipfile 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.
This catalog includes workflows based on the following criteria:
workflow/rulesthat folder must at least contain one file ending on
In order to additionally appear in the "standardized usage" area, repositories additionally have to
workflow/Snakefile(unlike for plain inclusion (see above), which also allows just
Snakefilein the root of the repository),
.snakemake-workflow-catalog.ymlin 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