Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cut-n-Run pipeline paired-end

Experimental pipeline for Cut-n-Run analysis. Uses mapping results from the following experiment types: - `chipseq-pe.cwl` - `trim-chipseq-pe.cwl` - `trim-atacseq-pe.cwl` Note, the upstream analyses should not have duplicates removed

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

Path: workflows/trim-chipseq-pe-cut-n-run.cwl

Branch/Commit ID: 1131f82a53315cca217a6c84b3bd272aa62e4bca
workflow graph js-expr-req-wf.cwl#wf

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7

Packed ID: wf
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_dispatch/2working_files/workflow.cwl

Branch/Commit ID: 7198756b4b1519d102178042924671bd677e9b17
workflow graph 3stepWorkflow.cwl

https://github.com/giannisdoukas/CWLJNIKernel.git

Path: tests/cwl/3stepWorkflow.cwl

Branch/Commit ID: e07959c147a9a4f5470f5ed3c22e37356ec92197
workflow graph CODEX analysis pipeline using Cytokit

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

Path: steps/ometiff_second_stitching.cwl

Branch/Commit ID: b23af942f4a1169fc3d331272fd56ae878af6c1d
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: 9850a859de1f42d3d252c50e15701928856fe774
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 02816f0d66e36c8eeba02d211cc90e36bf1c9df5
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: e2a6cbcc36212433d8fbc804919442787a5e2a49
workflow graph Filter single sample sv vcf from depth callers(cnvkit/cnvnator)

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

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe