Tool registration

After the reference and sample files are registered, the next step is to register a predefined workflow as a tool on the SeqsLab platform.

Objective

This tutorial will help you register a tool based on a GATK-Germline-Snps-Indels workflow from Dockstore.

Prerequisites

Before you begin, you will need the following:

• SeqsLab managed application on Azure. For details, see Test drive SeqsLab.

• A running instance of the SeqsLab CLI tool. For details, see Pull and run the SeqsLab CLI.

• A command line interface (CLI) tool such as the Windows Command Prompt or the Mac Terminal

1. Get the published workflow from Dockstore

Use the following command to get the workflow from Dockstore:

# get workflow.zip from dockstore
    mkdir working_dir && \
    wget https://dockstore.org/api/workflows/18394/zip/158152 \
    -O working_dir/workflow.zip
cd working_dir && unzip workflow.zip

The downloaded ZIP includes all the WDL files for the published tool.

tree
.
├── GATK-Germline-Snps-Indels
│   ├── execs
│   │   └── gatk.parallel.hg19.0713.execs.json
│   ├── inputs
│   │   └── GATK-Germline-Snps-Indels-inputs.json
│   └── wdl
│       ├── GATK-Germline-Snps-Indels-main.wdl
│       └── subworkflows
│           ├── haplotypecaller-gvcf-gatk4.wdl
│           ├── processing-for-variant-discovery-gatk4.wdl
│           └── tasks.wdl
└── workflow.zip

2. Register the tool

Use the tools tool command to register the workflow as a new tool.

export TOOL_ID="wgs_germline_gatk4_snp_indel_`date '+%Y%m%d%H%M%S'`"
seqslab tools tool \
    --id "${TOOL_ID}" \
    --name "testdrive-${TOOL_ID}" \
    --description "test drive workflow"

Use the tools version command to register a new tool version.

seqslab tools version \
    --descriptor-type WDL  \
    --tool-id "${TOOL_ID}" \
    --id "1.0" \
    --workspace "${WORKSPACE}" \
    --images '[{"image_type": "docker", "image_name": "atgenomix/seqslab_runtime-1.5_ubuntu-20.04_preprocessgatk4-4.2.0.0:2022-10-05-02-36", "registry_host": "tmuhwus24434bacr.azurecr.io", "size": 3349109245, "checksum": "sha256:020be4ed428c7dfec67d6c640aaec07d239406c1222295b22a8da6be2ec38ad1"}]'

Use the tools file command to upload tool files to the newly created tool version.

seqslab tools file \
    --descriptor-type WDL \
    --tool-id "${TOOL_ID}" \
    --version-id "1.0" \
    --working-dir `pwd`/GATK-Germline-Snps-Indels/ \
    --file-info execs/gatk.parallel.hg19.0713.execs.json