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
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:
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
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