Explore Workflows

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

Graph Name Retrieved From View
workflow graph Build Bowtie indices

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_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/bowtie-index.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Run genomic CMsearch

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph rMATS_bam_packed.cwl

https://github.com/Xinglab/rmats-turbo.git

Path: cwl/rMATS_bam_packed.cwl

Branch/Commit ID: fb6e269a0da3fc923ef437ef32d65bd04bc4d5eb
workflow graph Single-Cell WNN Cluster Analysis

Single-Cell WNN Cluster Analysis Clusters cells by similarity on the basis of both gene expression and chromatin accessibility data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” and “Single-Cell ATAC-Seq Dimensionality Reduction Analysis” pipelines run sequentially. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, “Single-Cell Differential Abundance Analysis”, “Single-Cell ATAC-Seq Differential Accessibility Analysis”, and “Single-Cell ATAC-Seq Genome Coverage” pipelines.

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

Path: workflows/sc-wnn-cluster.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Filter Protein Alignments

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

Path: protein_alignment/wf_align_filter.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph Single-Cell Label Integration Analysis

Single-Cell Label Integration Analysis Harmonizes conflicting annotations in single-cell genomics studies.

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

Path: workflows/sc-triangulate.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
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: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Seed Protein Alignments

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

Path: protein_alignment/wf_seed_seqids.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph Single-Cell RNA-Seq Cluster Analysis

Single-Cell RNA-Seq Cluster Analysis Clusters cells by similarity of gene expression data from the outputs of the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline. The results of this workflow are used in the “Single-Cell Manual Cell Type Assignment”, “Single-Cell RNA-Seq Differential Expression Analysis”, “Single-Cell RNA-Seq Trajectory Analysis”, and “Single-Cell Differential Abundance Analysis” pipelines.

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

Path: workflows/sc-rna-cluster.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895