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