sarek_plus_germline_dry
Curl
curl -X 'PUT' \
'http://localhost:8000/pipelines/' \
-H 'accept: application/json' \
-H 'Authorization: Bearer $token'
-H 'Content-Type: application/json' \
-d '{
"name": "ananda_plus_bag",
"analysis_type": "germline",
"data": {
"repo": "bag-cnag/sarek_plus_germline_dry",
"step": "mapping",
"steps": [
{
"step": "File availability and integrity",
"step_type": "process",
"description": ""
},
{
"step": "Sequencing data quality check",
"step_type": "qc",
"description": ""
},
{
"step": "Mapping to the reference genome",
"step_type": "process",
"description": ""
},
{
"step": "Mapping quality check",
"step_type": "qc",
"description": ""
},
{
"step": "Variant calling (SNV, CNV/SV) + Biomarkers/Pharmacogenomics",
"step_type": "process",
"description": ""
},
{
"step": "Variant calling quality check",
"step_type": "qc",
"description": ""
},
{
"step": "Annotations",
"step_type": "process",
"description": ""
},
{
"step": "Annotations Quality Check",
"step_type": "qc",
"description": ""
},
{
"step": "Upload to Elastic",
"step_type": "process",
"description": ""
},
{
"step": "Upload to Elastic Quality Check",
"step_type": "qc",
"description": ""
},
{
"step": "Pipeline completion check",
"step_type": "process",
"description": ""
}
],
"tools": "cnvkit,manta,haplotypecaller,strelka,expansionhunter,stripy,fullmetrics",
"pipelines": "sarek,pcgx,annotatesvs,gatk_mt,qualitycontrols"
}
}'