Explore Workflows

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: 449bc7e45bb02316d040f73838ef18359e770268

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8

Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-peak.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03

https://github.com/aplbrain/saber.git

Path: saber/i2g/examples/I2G_Seg_Workflow/workflowSegment.cwl

Branch/Commit ID: d370ce1afd6b25be764b35069262fa23bc8f9974

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

Path: tests/wf/wffail.cwl

Branch/Commit ID: eba80916b5cde8bdbd56c077c94240ddf796a27b

This workflow creates a subsample from a BAM file creating a tagAlign and pseudoreplicates

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/File-formats/subample-pseudoreplicates.cwl

Branch/Commit ID: 265440c63ab75d2451c90bcd116e725626e9a608

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: pipeline.cwl

Branch/Commit ID: c502823c0b078737ef4533b1509e25d58cb3a78a

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 9850a859de1f42d3d252c50e15701928856fe774

Run metrics workflow

https://github.com/Sentieon/Sentieon-cwl.git

Path: stage/metrics-flow.cwl

Branch/Commit ID: 845f4699c5fce96a4c708a553b3701c9cf296653

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

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

Branch/Commit ID: e67f19d8a713759d761ecad050966d1eb043b85c

Packed ID: wf