wdl-mkref

Generating a hybrid (human + mouse) scRNA-seq STAR reference:

• Human (GRCh38) / Ensembl 98
• Mouse (GRCm38) / Ensembl 98

Setup

Sharp 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 to create a reference package - one inputs file and one labels file. Use the following example files to help you create your job file:

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

Input

Note that a reference package created using STAR v2.5.3a is not compatible with STAR v2.7.6a or vice versa.

{
    "mkref.genomeVersion": "38",
    "mkref.ensemblVersion": "98",
    "mkref.sjdbOverhang": 101,
    "mkref.biotypes": [
        "protein_coding",
        "lincRNA",
        "antisense",
        "IG_V_gene",
        "IG_D_gene",
        "IG_J_gene",
        "IG_C_gene",
        "TR_V_gene",
        "TR_D_gene",
        "TR_J_gene",
        "TR_C_gene"
    ],
    "mkref.starVersion": "2.5.3a",
    "mkref.dockerRegistry": "quay.io/hisplan"
}

Submit Your Job

$ ./submit.sh \
    -k ~/keys/cromwell-secrets.json \
    -i configs/mkref-GRCh38-GRCm38-Ensembl98.inputs.json \
    -l configs/mkref-GRCh38-GRCm38-Ensembl98.labels.aws.json \
    -o mkref.options.aws.json