Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines6-wf.cwl

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

Path: tests/count-lines6-wf.cwl

Branch/Commit ID: main
workflow graph hi-c-processing-pairs-nore-nonorm.cwl

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

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

Branch/Commit ID: dev2
workflow graph get_spike_in_counts.cwl

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

Path: CWL/workflow_modules/get_spike_in_counts.cwl

Branch/Commit ID: master
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 64c3985e5ce7fa16ce7692faa879c5d58f31089f
workflow graph Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass4.cwl

Branch/Commit ID: 4a44218a713aecc488359be275409414ae8c1434
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 ValidateSinglePhotoElectronResponse

Validate single photon electron response.

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

Path: workflows/ValidateSinglePhotoElectronResponse.cwl

Branch/Commit ID: main
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: downsample_and_recall
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: downsample_and_recall
workflow graph facets

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/facets.cwl

Branch/Commit ID: dev