Explore Workflows

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

Graph Name Retrieved From View
workflow graph SV filtering workflow

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

Path: definitions/subworkflows/filter_sv_vcf.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5
workflow graph EMG pipeline v3.0 (paired end version)

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3-paired.cwl

Branch/Commit ID: caea457b17388fdc5cb088364c194504ae736bdd
workflow graph wrapped_workflow_example_workflow.cwl

https://github.com/Aeolic/example-workflow.git

Path: wrapped_workflow_example_workflow.cwl

Branch/Commit ID: 2471aac06dafdeaa606b02cc7a83a924036a061b
workflow graph amplicon_metrics.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/amplicon_metrics.cwl

Branch/Commit ID: 1046947f8d2923e6563b3aceac9e435554c5bea1
workflow graph filter_alignment_artifacts.cwl

GATK4.1.2 Alignment artifacts filtration workflow

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

Path: subworkflows/filter_alignment_artifacts.cwl

Branch/Commit ID: 58b62b1bf329b3fbffbd5d9080709999bebc1763
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 0805e8e0d358136468e0a9f49e06005e41965adc
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