SCRNA-CWL Workflow

This workflow processes single cell RNA sequencing data from the 10X Genomics Platform. None of the tools or files in this repository are provided or supported by 10X Genomics. SCRNA-CWL performs the following tasks:

• Creates a csv report of basic input data provenance (synapseid, file version numbers)
• Groups input fastq files based on the specimen ID provided in the Synapse annotation
• Downloads input fastq files using the Synapse Python Client
• Performs molecule counting using the cellranger count function
• Aggregates gene counts across specimen using the cellranger aggr function
• Uploads results to a specified Synapse with appropriate provenance

Workflow Dependencies

To execute this workflow, input fastq files must be present in a Synapse folder and each file must contain an annotation for the specimenId field. In addition, the following dependencies must be installed:

• Docker
• A workflow execution engine that is compatible with CWL. Examples include cwl-tool and Toil

Execution with cwltool

To execute a test workflow that contains non-phi data from the SRA archive, execute the following command:

cwl-runner fastq_to_counts.cwl jobs/test_SRA/job.json

Execution with toil

To execute a test workflow that contains non-phi data from the SRA archive, create a toil cluster and execute the following command:

./run-toil.py jobs/test_SRA