Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph Kallisto index pipeline

This workflow indexes the input reference FASTA with kallisto, and generates a kallisto index file (.kdx). This index sample can then be used as input into the kallisto transcript-level quantification workflow (kallisto-quant-pe.cwl), or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed - number of threads to use for multithreading processes ### __Outputs__ - kallisto index file (.kdx). - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-kallisto to index reference FASTA with `kallisto index`, generating a kallisto index file. ### __References__ - Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519

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

Path: workflows/kallisto-index.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895