Explore Workflows

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

Graph Name Retrieved From View
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: c6bfa0de917efb536dd385624fc7702e6748e61d
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: a70a83fe14a100cd16e2402ec17b2904f5eeb17d
workflow graph annotate.cwl

https://github.com/hubmapconsortium/hra-workflows.git

Path: steps/annotate.cwl

Branch/Commit ID: 9de19547a66b5b705c16de616da2dced5c9175f8
workflow graph conflict.cwl#main

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

Path: tests/wf/conflict.cwl

Branch/Commit ID: dbc4c4c2ad30ed31367b4fbcc3bb4084fdcabaa2

Packed ID: main
workflow graph scatter-valuefrom-wf1.cwl

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

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph DiffBind - Differential Binding Analysis of ChIP-Seq Peak Data

Differential Binding Analysis of ChIP-Seq Peak Data --------------------------------------------------- DiffBind processes ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. It is designed to work with multiple peak sets simultaneously, representing different ChIP 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: 664de58d95728edbf7d369d894f9037ebe2475fa
workflow graph GATK4_SomaticVariantCaller_4_1_3_0.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/GATK4_SomaticVariantCaller_4_1_3_0.cwl

Branch/Commit ID: c1aeec7b68acdd1eab3f1d1bd75d768e31abd6d2
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 29bf638904709cfbf10908adcd51ba4886ace94a
workflow graph Deprecated. Seurat Cluster

Deprecated. Seurat Cluster ========================== Runs filtering, integration, and clustering analyses for Cell Ranger Count Gene Expression or Cell Ranger Aggregate experiments.

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

Path: workflows/seurat-cluster.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e