Explore Workflows

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

Graph Name Retrieved From View
workflow graph mut.cwl

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

Path: tests/wf/mut.cwl

Branch/Commit ID: 596aab620489cd2611f4bc1d9a4fc914ddf34514
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: d87a0786b52809b36201adb7d3d3ab2b8bbbef20
workflow graph tt_univec_wnode.cwl

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

Path: task_types/tt_univec_wnode.cwl

Branch/Commit ID: a3affd1b9e3e16f0644a25fee1a7b87b99df57b0
workflow graph Cell Ranger Count (RNA+VDJ)

Cell Ranger Count (RNA+VDJ) Quantifies single-cell gene expression, performs V(D)J contigs assembly and clonotype calling of the sequencing data from a single 10x Genomics library in a combined manner. The results of this workflow are primarily used in either “Single-Cell RNA-Seq Filtering Analysis”, “Single-Cell Immune Profiling Analysis”, or “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines.

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

Path: workflows/cellranger-multi.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph count-lines13-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines13-wf.cwl

Branch/Commit ID: beab66d649dd3ee82a013322a5e830875e8556ba
workflow graph STAR-RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq_star_fusion.cwl

Branch/Commit ID: 35e6b3ef71b4a2a9caba1dbd5dc424a8809bcc0a
workflow graph trim-rnaseq-pe-dutp.cwl

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

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

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: dc4ee45ed2c5c30e9a1a173c9ea4445f27d3788a
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: d87a0786b52809b36201adb7d3d3ab2b8bbbef20
workflow graph Generate genome indices for STAR & bowtie

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: d6f58c383d0676269afb519399061191a1144a6a
workflow graph search.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: beab66d649dd3ee82a013322a5e830875e8556ba

Packed ID: main