Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	workflow.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_apollo2_data_processing/processing/workflow.cwl Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729
	SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.	https://github.com/datirium/workflows.git Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
	somatic_exome: exome alignment and somatic variant detection somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_exome.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
	downsample unaligned BAM and align	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
	variant-calling-pair.cwl	https://github.com/mskcc/argos-cwl.git Path: modules/pair/variant-calling-pair.cwl Branch/Commit ID: 54c9e02751dc65607f0e334c0eb1a5e646cc71d6
	picard_markduplicates Mark duplicates	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/picard_markduplicates.cwl Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e
	exome alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
	bwa_mem	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/bwa_mem.cwl Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e
	genomics-workspace-cds.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_genomicsWorkspace/genomics-workspace-cds.cwl Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729
	cnv_exomedepth CNV ExomeDepth calling	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e