Single-cell Expression Atlas control workflow for single-cell expression data analysis

This is a Nextflow workflow which:

• Derives configuration from an SDRF file
• Determines protocol and associated settings
• Runs quantifications appropriate to the protocol
• Aggregates resulting matrices
• If specified, Runs downstream analysis using Scanpy, leveraging the scanpy-scripts package to run individual steps of the Scanpy workflow.

It's actually a workflow-of-workflows comprising:

• scxa-smartseq-quantification-workflow
• scxa-aggregation-workflow
• Clustering using Scanpy, via Galaxy workflows encoded here
• scxa-bundle-workflow

Setup

Conda/ Bioconda

Workflow dependencies are managed via Conda and Bioconda, so you'll need to set that up, see instructions here.

Nextflow

Obviously you'll need Nextflow itself. If you don't have it already you can install via Conda:

conda install nextflow

You may well want to do this within a Conda environment you create for the purpose.

Workflows

Clone this repo into a directory called 'workflow' under the directory from where you will execute it, such that you have (RUN DIR)/workflow/scxa-control-workflow.

You will also need to clone scxa-workflows, which contains child workflows as submodules, and acts as a central place to store parameters. Clone it under the same directory, so that you have (RUN DIR)/workflow/scxa-workflows.

Job scheduling and workload management system

Current config setup for SLURM.

Run the workflow

Routine analysis is triggered (from the above directories) like:

./workflow/scxa-control-workflow/bin/submitControlWorkflow.sh -t scanpy-galaxy

This will look for SDRF files in the directory specified by the environment variable SCXA_SDRF_DIR, triggering analyses for any new experiments found there, running quantifications via Nextflow child workflows, and tertiary analysis via the API to a Galaxy setup.

Outputs

Outputs will be placed in the directory defined as SCXA_RESULTS under 'env' in nextflow.config ('results' by default).