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/146282 \
-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_gatk4:v3", "registry_host": "seqslabmain.azurecr.io", "size": 3237188921, "checksum": "sha256:1e188b37ba11d265d15107c67a40a43fd831d2a914fe02587a6cc8027be676fa"}]'
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