Explore Workflows

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

Graph Name Retrieved From View
workflow graph DiffBind - Differential Binding Analysis of ChIP-Seq or CUTß&RUN/Tag Peak Data

Differential Binding Analysis of ChIP-Seq or CUT&RUN/Tag Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq or CUT&RUN/Tag data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by peak caller tools and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP or CUT&RUN/Tag experiments (antibodies, transcription factor and/or histone marks, experimental conditions, replicates) as well as managing the results of multiple peak callers. For more information please refer to: ------------------------------------- Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S, Palmieri C, Caldas C, Carroll JS (2012). “Differential oestrogen receptor binding is associated with clinical outcome in breast cancer.” Nature, 481, -4.

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

Path: workflows/diffbind.cwl

Branch/Commit ID: bf80c9339d81a78aefb8de661bff998ed86e836e
workflow graph count-lines3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
workflow graph count-lines17-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines17-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
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: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph super-enhancer.cwl

Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph io-int-optional-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/io-int-optional-wf.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph Single-cell ATAC-Seq Genome Coverage

Single-cell ATAC-Seq Genome Coverage Creates genome coverage bigWig files from the provided fragments file and selected grouping parameters

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

Path: workflows/sc-atac-coverage.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fastq.workflow.cwl

Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4
workflow graph Cell Ranger Count Gene Expression

Cell Ranger Count Gene Expression =================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe