Usage

This section provides some simple usage examples. For more information what the workflow does, see Single-cell RNA sequencing workflow.

Running the wrapper script

lts_workflows_sm_scrnaseq comes with a wrapper script that calls snakemake and provides additional help messages. Running the wrapper without any arguments will generate a help message. If any arguments are provided they are passed on to snakemake.

$ lts_workflows_sm_scrnaseq
$ lts_workflows_sm_scrnaseq -l
$ lts_workflows_sm_scrnaseq all
$ lts_workflows_sm_scrnaseq --use-conda all
$ lts_workflows_sm_scrnaseq -s /path/to/Snakefile --use-conda all

If no Snakefile is provided, the wrapper script will automatically load the Snakefile from the package root directory (see example_snakefile). Note that you will have to pass a configuration file with the –configfile parameter.

In the case you need to add custom rules, or want to hardcode parameters such as the working directory and configuration file, you can of course copy and edit the provided Snakefile.

Running snakemake

You can of course bypass the provided wrapper script and run snakemake directly on your own Snakefile. If so, the intended usage is to include the main workflow file in a Snakefile. See the examples in the test directory.

$ snakemake -s Snakefile -d /path/to/workdir --configfile config.yaml all

Running docker/singularity containers

Note

Singularity is still WIP.

lts_workflows_sm_scrnaseq is also shipped with all the dependencies packaged in a docker image. This eliminates some of the installation issues, at the cost of having to download a large image file (>5GB). In any case, the entry point of the image points to the lts_workflows_sm_scrnaseq wrapper script.

$ docker pull scilifelablts/lts_workflows_sm_scrnaseq
$ docker run scilifelablts/lts_workflows_sm_scrnaseq
$ docker run -v /path/to/workdir:/workspace -w /workspace scilifelablts/lts_workflows_sm_scrnaseq -l
$ docker run -v /path/to/workdir:/workspace -w /workspace scilifelablts/lts_workflows_sm_scrnaseq all

Example Snakefile

The provided minimum Snakefile looks as follows:

# -*- snakemake -*-
from lts_workflows_sm_scrnaseq import WORKFLOW

include: WORKFLOW