Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: 700e73aaed6db1ad538dd27b2e1709f436ad3edb
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