Explore Workflows

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

Graph Name Retrieved From View
workflow graph Nested workflow example

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/nested.cwl

Branch/Commit ID: f94719e862f86cc88600caf3628faba6c0d05042
workflow graph BWA index pipeline

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

https://github.com/datirium/workflows.git

Path: workflows/bwa-index.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph Pairwise genomic regions intersection

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

 https://github.com/datirium/workflows.git

Path: workflows/peak-intersect.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph step-valuefrom5-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/step-valuefrom5-wf.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4
workflow graph count-lines7-single-source-wf_v1_0.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/count-lines7-single-source-wf_v1_0.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a
workflow graph count-lines7-wf_v1_0.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/count-lines7-wf_v1_0.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355
workflow graph Cell Ranger Aggregate (RNA+ATAC)

Cell Ranger Aggregate (RNA+ATAC) Combines outputs from multiple runs of “Cell Ranger Count (RNA+ATAC)” pipeline. The results of this workflow are primarily used in “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipeline.

 https://github.com/datirium/workflows.git

Path: workflows/cellranger-arc-aggr.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28
workflow graph Workflow that executes the Sounder SIPS end-to-end L1b processing

Requires valid AWS credentials as input arguments

 https://github.com/unity-sds/unity-sps-workflows.git

Path: sounder_sips/ssips_L1b_workflow.cwl

Branch/Commit ID: 40117db4f27a7dd24407b06f2a6f18388002f12c
workflow graph workflow_same_level_v2.cwl#main_pipeline

Simulation steps pipeline

 https://github.com/ILIAD-ocean-twin/application_package.git

Path: workflow_in_workflow/workflow_same_level_v2.cwl

Branch/Commit ID: c7009260d3d659b77148dff5cd79b71d0e01ff41

Packed ID: main_pipeline