Explore Workflows

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

Graph Name Retrieved From View
workflow graph Single-Cell RNA-Seq Dimensionality Reduction Analysis

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

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

Path: workflows/sc-rna-reduce.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Single-Cell Manual Cell Type Assignment

Single-Cell Manual Cell Type Assignment Assigns identities to cells clustered with any of the “Single-Cell Cluster Analysis” pipelines. For “Single-Cell RNA-Seq Cluster Analysis” the results of this workflow are used in the “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, and — when combined with outputs from the “Cell Ranger Count (RNA+VDJ)” or “Cell Ranger Aggregate (RNA, RNA+VDJ)” workflow — in the “Single-Cell Immune Profiling Analysis” pipeline. For “Single-Cell ATAC-Seq Cluster Analysis”, the results of this workflow are used in the “Single-Cell ATAC-Seq Differential Accessibility Analysis” and “Single-Cell ATAC-Seq Genome Coverage” pipelines. For “Single-Cell WNN Cluster Analysis”, the results of this workflow are used in all of the above, except the “Single-Cell Immune Profiling Analysis” pipeline.

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

Path: workflows/sc-ctype-assign.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 0d0ba0c3410e8aee55c82f077cee31d8ee929b5a
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e
workflow graph sum-wf.cwl

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

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

Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de
workflow graph trim-chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

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

Path: workflows/trim-chipseq-pe.cwl

Branch/Commit ID: 568da91bb1c6182ba4f146e2a729cac1c3d8783c
workflow graph Replace legacy AML Trio Assay

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

Path: definitions/pipelines/cle_aml_trio.cwl

Branch/Commit ID: 735be84cdea041fcc8bd8cbe5728b29ca3586a21
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: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph default-dir5.cwl

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

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: cd1ba3df3745fba4b635f05c67ebeaf3b8a9f4ec