wdl-cellranger-vdj

WDLized Cell Ranger V(D)J 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:

• config/template.inputs.json
• config/template.labels.json

Inputs

Note that the prefix CellRangerVdj. is omitted for brevity.

• referenceGenome
  • Specify a reference to be used:
    • GRCh38: Human
    • GRCm38: Mouse
• chain
  • Force the analysis to be carried out for a particular chain type. The accepted values are:
    • auto: autodetection based on TR vs. IG representation
    • TR: T cell receptors
    • IG: B cell receptors

Submit Your Job

conda activate scing

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