Explore Workflows

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

Graph Name Retrieved From View
workflow graph Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph Pairwise genomic regions intersection

Pairwise genomic regions intersection ============================================= Overlaps peaks from two ChIP/ATAC experiments

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

Path: workflows/peak-intersect.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph Seurat for comparative scRNA-seq analysis of across experimental conditions

Runs Seurat for comparative scRNA-seq analysis of across experimental conditions ================================================================================

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

Path: workflows/seurat-cluster.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph samtools_mpileup_subpipeline.cwl

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

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

Branch/Commit ID: d3ae7483f860339a12c5f404de9db0f026571f77
workflow graph umi duplex alignment workflow

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9
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: 935a78f1aff757f977de4e3672aefead3b23606b
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc
workflow graph alignment for nonhuman with qc

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

Path: definitions/pipelines/alignment_wgs_nonhuman.cwl

Branch/Commit ID: 174f3b239018328cec1d821947438b457552724c
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 3d280a2a4b4f1560f56991086f712fa22ddc3364
workflow graph consensus_maf.cwl

Workflow to merge a large number of maf files into a single consensus maf file for use with GetBaseCountsMultiSample

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

Path: cwl/consensus_maf.cwl

Branch/Commit ID: 5cad957fec135aa55ca8d588372db0557ca1cad5