Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

Packed ID: main
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: c6bfa0de917efb536dd385624fc7702e6748e61d
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: 7c7615c44b80f8e76e659433f8c7875603ae0b25
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 2dce710246e091f0189fab41b589ee062ee94500
workflow graph secret_wf.cwl

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: 2dce710246e091f0189fab41b589ee062ee94500
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 051074fce4afd9732ef34db9dd43d3a1d8e979d6
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: c28cfb9882dedd3c522160f933cff1050ae24100
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq_alignment.cwl

Branch/Commit ID: 6f9f8a2057c6a9f221a44559f671e87a75c70075
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: c28cfb9882dedd3c522160f933cff1050ae24100
workflow graph adapter for sequence_align_and_tag

Some workflow engines won't stage files in our nested structure, so parse it out here

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

Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca