Explore Workflows

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

Graph Name Retrieved From View
workflow graph simple_magicblast.cwl

https://github.com/ncbi/cwl-demos.git

Path: blast-pipelines/simple_magicblast.cwl

Branch/Commit ID: master
workflow graph validate_interleaved_fq.cwl

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/validate_interleaved_fq.cwl

Branch/Commit ID: 0.3.0
workflow graph panel of normals workflow

https://github.com/hamid58b/cancer-genomics-workflow.git

Path: panel_of_normals/workflow.cwl

Branch/Commit ID: master
workflow graph rp2-to-rp2path.cwl

https://github.com/alaninmcr/test-cwl.git

Path: workflows/rp2-to-rp2path.cwl

Branch/Commit ID: master
workflow graph TOPMed_RNA-seq

TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows) 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/FarahZKhan/cwl_workflows.git

Path: topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl

Branch/Commit ID: CWLProvTesting
workflow graph parallel_no_threshold.cwl

https://github.com/yuandou168/FL_workflows.git

Path: workflows/parallel_no_threshold.cwl

Branch/Commit ID: main
workflow graph cnv_exomedepth

CNV ExomeDepth calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/cnv_exome_depth.cwl

Branch/Commit ID: 1.1.3
workflow graph 03-map-pe.cwl

ChIP-seq 03 mapping - reads: PE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/03-map-pe.cwl

Branch/Commit ID: master
workflow graph final_filtering

Final filtering

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/final_filtering.cwl

Branch/Commit ID: master
workflow graph Protein_Inference_workflow.cwl

https://github.com/adamscharlotte/CWL-workflow.git

Path: Protein_Inference_workflow.cwl

Branch/Commit ID: master