Explore Workflows

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

Graph Name Retrieved From View
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: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd
workflow graph example_workflow.cwl

Example CWL workflow that uses some advanced features

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

Path: cwl/example_workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph FastQC - a quality control tool for high throughput sequence data

FastQC - a quality control tool for high throughput sequence data ===================================== FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are: - Import of data from FastQ files (any variant) - Providing a quick overview to tell you in which areas there may be problems - Summary graphs and tables to quickly assess your data - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application

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

Path: workflows/fastqc.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2
workflow graph iwdr_with_nested_dirs.cwl

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63
workflow graph Filter differentially expressed genes from DESeq for Tag Density Profile Analyses

Filters differentially expressed genes from DESeq for Tag Density Profile Analyses ================================================================================== Tool filters output from DESeq pipeline run for genes to create a file with regions of interest for Tag Density Profile Analyses.

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

Path: workflows/filter-deseq-for-heatmap.cwl

Branch/Commit ID: 57863b6131d8262c5ce864adaf8e4038401e71a2
workflow graph Detect Variants workflow for nonhuman WGS pipeline

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

Path: definitions/pipelines/detect_variants_wgs_nonhuman.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 0c4f4e59c265eb22aed3d2d37b173cb5430773d2
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 76a9637a06e2102645eae29aff10b6f7185892a5
workflow graph Seed Protein Alignments

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

Path: protein_alignment/wf_seed_seqids.cwl

Branch/Commit ID: 369e2b6c7f4db75099d258729dec1326f55d2cc5
workflow graph schemadef-wf.cwl

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

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

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621