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. The following section provides step-by-step instructions on how to register a tool based on the GATK-Germline-Snps-Indels workflow published on Dockstore.

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

Register the tool#

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

seqslab tools version \
    --descriptor-type WDL  \
    --tool-id "${TOOL_ID}" \
    --id "1.0" \
    --workspace "${WORKSPACE}" \
    --images '[{"image_type": "docker", "image_name": "atgenomix/seqslab_runtime-1.4_ubuntu-18.04_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 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