Explore Workflows

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

Graph Name Retrieved From View
workflow graph 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: 700e73aaed6db1ad538dd27b2e1709f436ad3edb
workflow graph Report generation workflow

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/helper/report-wf.cwl

Branch/Commit ID: f80667171aa3d9efb35d60faa4d9cdabb50ca330
workflow graph Replace legacy AML Trio Assay

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: e8b7759826df40b8bb821b40b15aea960a4951c4
workflow graph Tumor-Only Detect Variants workflow

https://github.com/litd/analysis-workflows.git

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 193b8de694f262ad55c7635a603c20c124748583
workflow graph CODEX analysis pipeline using Cytokit

https://github.com/hubmapconsortium/codex-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: 2d9ddc61af332c2be63e4a519d9769813f3cc57d
workflow graph exome alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
workflow graph Example of setting up a simulation system

CWL version of the md_list.cwl workflow for HPC.

https://github.com/douglowe/biobb_hpc_cwl_md_list.git

Path: md_list.cwl

Branch/Commit ID: 95111f381617c8e63794eca42d06f10ed2605f4f
workflow graph WGS processing workflow scattered over samples

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/wgs-processing-wf.cwl

Branch/Commit ID: 7521f8770b81d944aad3c1e0fd7ef5a886600190
workflow graph exome alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: e8b7759826df40b8bb821b40b15aea960a4951c4
workflow graph wgs alignment and tumor-only variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/tumor_only_wgs.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0