Explore Workflows

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

Graph Name Retrieved From View
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: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph format_rrnas_from_seq_entry

https://github.com/ncbi/pgap.git

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa
workflow graph kmer_cache_store

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0
workflow graph kmer_ref_compare_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: c28cfb9882dedd3c522160f933cff1050ae24100
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: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph trim-chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-chipseq-se.cwl

Branch/Commit ID: de847468843203ce92b6d19323c5fe77dc488e34
workflow graph project-workflow-sv.cwl

https://github.com/mskcc/argos-cwl.git

Path: project-workflow-sv.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6
workflow graph project-workflow.cwl

https://github.com/mskcc/argos-cwl.git

Path: project-workflow.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6
workflow graph structural-variants-pair.cwl

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/structural-variants-pair.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6
workflow graph GATKBaseRecalBQSRWorkflow_4_1_3.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl

Branch/Commit ID: b4550175be9d485d509c61d87fddf88a8bdb70c1