Workflows V1
Workflows associated with version 1 of the Assay
BAM Generation & Quality Control
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/ACCESS_pipeline.cwl
Tools Used:
Variant Calling
Small Variants
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/snps_and_indels.cwl
Tools Used:
Copy Number Variant (CNV)
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/call_cnv.cwl
Refer to Bioinformatics Pipeline to Detect CNA's section in this paper for details:
Structural Variant (SV)
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/manta.cwl
Tool Used:
Microsatellite Instability Status (MSI)
Github Location -> https://github.com/mskcc/ACCESS-Pipeline/blob/master/workflows/subworkflows/msi.cwl
Tool Used:
Configurations
Voyager has all our configurations in the jinja template, it includes all the paths for various files and tools associated with the workflows, all location are on JUNO:
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