Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cell Ranger Reference (VDJ)

Cell Ranger Reference (VDJ) Builds a reference genome of a selected species for V(D)J contigs assembly and clonotype calling. The results of this workflow are used in “Cell Ranger Count (RNA+VDJ)” pipeline.

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

Path: workflows/cellranger-mkvdjref.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph count-lines10-wf.cwl

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

Path: tests/count-lines10-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph sum-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/sum-wf.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a
workflow graph conflict-wf.cwl#collision

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389

Packed ID: collision
workflow graph scatter-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a

Packed ID: main
workflow graph env-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b
workflow graph env-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf2.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a
workflow graph exomeseq-gatk4-01-preprocessing.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-gatk4-01-preprocessing.cwl

Branch/Commit ID: 216ff9bf78130add564f7bcfba6385d5dab4c77d
workflow graph ROSE: rank ordering of super-enhancers

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 564156a9e1cc7c3679a926c479ba3ae133b1bfd4