Explore Workflows

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

Graph Name Retrieved From View
workflow graph exomeseq-gatk4-02-variantdiscovery.cwl

https://github.com/bespin-workflows/exomeseq-gatk4.git

Path: subworkflows/exomeseq-gatk4-02-variantdiscovery.cwl

Branch/Commit ID: v2.0.3
workflow graph RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

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

Path: workflows/rna-selector.cwl

Branch/Commit ID: 2104dc3
workflow graph ValidateArrayElementCoordinates

Plot and compare array element coordinates. Validate coordinate transformation from those used in observatory database to simulation systems.

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

Path: workflows/ValidateArrayElementCoordinates.cwl

Branch/Commit ID: main
workflow graph scatter-valuefrom-wf4.cwl#main

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: main

Packed ID: main
workflow graph hi-c-processing-pairs.cwl

https://github.com/4dn-dcic/pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-pairs.cwl

Branch/Commit ID: dev2
workflow graph trim_and_map.cwl

https://github.com/CompEpigen/ATACseq_workflows.git

Path: CWL/workflow_modules/trim_and_map.cwl

Branch/Commit ID: master
workflow graph EMG pipeline v3.0 (single end version)

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

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 0746e12
workflow graph TOPMed_RNA-seq

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL) Pipeline steps: 1. Align RNA-seq reads with [STAR v2.5.3a](https://github.com/alexdobin/STAR). 2. Run [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). 2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6](https://github.com/samtools/samtools/releases) index. 3. Transcript quantification with [RSEM 1.3.0](https://deweylab.github.io/RSEM/) 4. Gene quantification and quality control with [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc)

https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git

Path: workflow/rnaseq_pipeline_fastq.cwl

Branch/Commit ID: master
workflow graph prefetch_fastq.cwl

Worfklow combining an SRA fetch from NCBI with a fastq-dump cmd

https://github.com/svonworl/bio-cwl-tools.git

Path: sratoolkit/prefetch_fastq.cwl

Branch/Commit ID: release
workflow graph metabarcode (gene amplicon) analysis for fastq files

protein - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/metabarcode-fastq.workflow.cwl

Branch/Commit ID: master