Explore Workflows

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

Graph Name Retrieved From View
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 0d0ba0c3410e8aee55c82f077cee31d8ee929b5a
workflow graph mini-ST610106.cwl

https://github.com/Marco-Salvi/dtc61.git

Path: mini-ST610106.cwl

Branch/Commit ID: 11824ff538109de2f553f836903b32c975873adb
workflow graph Salmon quantification, FASTQ -> H5AD count matrix

https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git

Path: salmon-rnaseq/steps/salmon-quantification.cwl

Branch/Commit ID: 68e0cc1be35751f5ef5958050742ddfffd564d3c
workflow graph PGAP Pipeline, simple user input, PGAPX-134

PGAP pipeline for external usage, powered via containers, simple user input: (FASTA + yaml only, no template)

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

Path: pgap.cwl

Branch/Commit ID: 61eaea2f746c8a1fc2a2b731056b068e28ca4e20
workflow graph Raw sequence data to BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
workflow graph WGS QC workflow mouse

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

Path: definitions/subworkflows/qc_wgs_mouse.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5
workflow graph 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: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Genelists heatmap - RNA-seq expression data visualized

# Genelists heatmap - RNA-seq expression data visualized This visualization workflow takes as input 1 or more genelists derived from the DESeq and/or diffbind workflows along with user-selected samples and visualizes RNA-Seq expression data in a single morpheus heatmap. ### __References__ - Morpheus, https://software.broadinstitute.org/morpheus

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

Path: workflows/genelists-deseq-only.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Single-Cell ATAC-Seq Dimensionality Reduction Analysis

Single-Cell ATAC-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of chromatin accessibility data from the outputs of “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell ATAC-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines.

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

Path: workflows/sc-atac-reduce.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph WGS and MT analysis for fastq files

rna / protein - qc, preprocess, filter, annotation, index, abundance

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

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

Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4