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Graph	Name	Retrieved From	View
	Unaligned BAM to BQSR	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/bam_to_bqsr.cwl Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
	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: e0a30aa1ad516dd2ec0e9ce006428964b840daf4
	03-map-pe.cwl ATAC-seq 03 mapping - reads: PE	https://github.com/Duke-GCB/GGR-cwl.git Path: v1.0/ATAC-seq_pipeline/03-map-pe.cwl Branch/Commit ID: 8d02684ae0ff27e641f3704686e3bc8b1979b854
	kmer_ref_compare_wnode	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_ref_compare_wnode.cwl Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da
	Subworkflow that runs cnvkit in single sample mode and returns a vcf file	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
	mosdepth_to_coverage_QC.cwl	https://github.com/YinanWang16/tso500-ctdna-post-processing.git Path: cwl/workflows/mosdepth_to_coverage_QC.cwl Branch/Commit ID: 2d9d8ae9a789a4b037b65dd1958649023b3d35c8
	tt_kmer_top_n.cwl	https://github.com/ncbi/pgap.git Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: be5ae41801b19ebc69a2889d8fdb39e8e2359611
	exome alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/tumor_only_exome.cwl Branch/Commit ID: 74647cc0f1abac4ee22950cfa89c44cf2ca3cffd
	exomeseq-gatk4-03-organizedirectories.cwl	https://github.com/Duke-GCB/bespin-cwl.git Path: subworkflows/exomeseq-gatk4-03-organizedirectories.cwl Branch/Commit ID: e82f3a71183048dd6700ec6725ee526ac1a95238
	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: e0a30aa1ad516dd2ec0e9ce006428964b840daf4