Explore Workflows

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

Graph Name Retrieved From View
workflow graph bulk-atac-seq-pipeline.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: bulk-atac-seq-pipeline.cwl

Branch/Commit ID: 53415520f94ac0d9a1fae89af0f6e8250240723a
workflow graph cond-wf-012_nojs.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-012_nojs.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
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: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph PCA - Principal Component Analysis

Principal Component Analysis --------------- Principal component analysis (PCA) is a statistical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables (entities each of which takes on various numerical values) into a set of values of linearly uncorrelated variables called principal components. The calculation is done by a singular value decomposition of the (centered and possibly scaled) data matrix, not by using eigen on the covariance matrix. This is generally the preferred method for numerical accuracy.

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

Path: workflows/pca.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: b4a6e46405c08e0b14ad92f0ab38bcc4a69caa5c
workflow graph gathered exome alignment and somatic variant detection

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

Path: definitions/pipelines/gathered_somatic_exome.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 5c40c5a0464c84076e0e407a0e05522b43bdc0a6
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/mr-c/datirium-workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 12b5d227a83b71aff941f50393df0c2c2002c336
workflow graph calculate_contamination_workflow.cwl

GATK4.1.2 Calculate tumor-normal contamination workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/calculate_contamination_workflow.cwl

Branch/Commit ID: 58b62b1bf329b3fbffbd5d9080709999bebc1763