wdl-cellranger-atac

WDLized Cell Ranger ATAC Pipeline

License

The code is available to everyone under the standard MIT license. However, the code internally uses 10x software, so please make sure that you read and agree to 10x End User Software License.

Setup

The pipeline is a part of SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/). For setup, please refer to this page. All the instructions below is given under the assumption that you have already configured SCING in your environment.

Create Job Files

You need two files for processing a V(D)J sample - one inputs file and one labels file. Use the following example files to help you create your configuration file:

configs/template.inputs.json
configs/template.labels.json

Reference

Use one of the URLs below for the reference genome:

Type	`CellRangerATAC.reference`
GRCh38	`https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-arc-GRCh38-2020-A-2.0.0.tar.gz`
mm10	`https://cf.10xgenomics.com/supp/cell-atac/refdata-cellranger-arc-mm10-2020-A-2.0.0.tar.gz`

Multiome

If you want to process the ATAC product of the multiome using Cell Ranger ATAC v2 (i.e. without GEX), you must set the following in the job config file:

"CellRangerATAC.chemistry": "ARC-v1"

Submit Your Job

conda activate scing

./submit.sh \
    -k ~/keys/cromwell-secrets.json \
    -i configs/your-sample.inputs.json \
    -l configs/your-sample.labels.json \
    -o CellRangerATAC.options.aws.json