Explore Workflows

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

Graph Name Retrieved From View
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba
workflow graph AltAnalyze Iterative Clustering and Guide-gene Selection

Devel version of AltAnalyze Iterative Clustering and Guide-gene Selection =========================================================================

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

Path: workflows/altanalyze-icgs.cwl

Branch/Commit ID: a1f6ca50fcb0881781b3ba0306dd61ebf555eaba
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: ae75b938e6e8ae777a55686bbacad824b3c6788c
workflow graph js-expr-req-wf.cwl#wf

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: 03af16c9df2ee77485d4ab092cd64ae096d2e71c

Packed ID: wf
workflow graph scatter-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl

Branch/Commit ID: 3e9bca4e006eae7e9febd76eb9b8292702eba2cb
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: 2c486543c335bb99b245dfe7e2f033f535efb9cf
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 2710cfe731374cf7244116dd7186fc2b6e4af344
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e
workflow graph Unaligned BAM to BQSR

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: a7838a5ca72b25db5c2af20a15f34303a839980e