Explore Workflows

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

Graph Name Retrieved From View
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 87f213456b3f966b773d396cce1fe5a272dad858
workflow graph 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/rnaseq-pe-dutp.cwl

Branch/Commit ID: 801f7b363e0599b9a28ecda696dfdb1c0e40ce71
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: 609aead9804a8f31fa9b3dbc7e52105aec487f31
workflow graph ROSE: rank ordering of super-enhancers

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_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/star-index.cwl

Branch/Commit ID: 17a4a68b20e0af656e09714c1f39fe761b518686
workflow graph scatterfail.cwl

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b
workflow graph advanced-header.cwl

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

Path: metadata/advanced-header.cwl

Branch/Commit ID: e846c74478ca8bf610fefc4b0ee1b3ecc7a5ccd1
workflow graph fail-wf.cwl

Run failtool which will fail

 https://github.com/Duke-GCB/calrissian.git

Path: input-data/fail-wf.cwl

Branch/Commit ID: 367e35ceabf68ab49e8097075abb0471d84a7fde
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: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e
workflow graph wf.cwl

https://github.com/ResearchObject/runcrate.git

Path: cwl/multisource/wf.cwl

Branch/Commit ID: 802bd3c43696c88821f75c3ec528573e06679521