Explore Workflows

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

Graph Name Retrieved From View
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.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/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 somatic_subpipeline.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/somatic_subpipeline.cwl

Branch/Commit ID: master
workflow graph forome_vcf_upload_archive.cwl

https://github.com/ForomePlatform/vcf-upload-cwl-pipeline.git

Path: forome_vcf_upload_archive.cwl

Branch/Commit ID: main
workflow graph word-mapping-dir.cwl#main

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/word-mapping-dir.cwl

Branch/Commit ID: master

Packed ID: main
workflow graph cmsearch-multimodel.cwl

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

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: master
workflow graph preprocess_vcf.cwl

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: preprocess_vcf.cwl

Branch/Commit ID: master
workflow graph nestedworkflows.cwl

https://github.com/common-workflow-language/user_guide.git

Path: src/_includes/cwl/workflows/nestedworkflows.cwl

Branch/Commit ID: main
workflow graph wf_simulate_data_collection.cwl

https://github.com/idaks/cwl_modeling.git

Path: yw_cwl_modeling/yw2cwl_parser/example_sql/simulate_data_collection/wf_simulate_data_collection.cwl

Branch/Commit ID: master
workflow graph epos single download

EPOS-IT Curl Workflow: downloads data based on curl input.

 https://github.com/andrejsim/epos-cwl-workflows.git

Path: epos_accept_single_url_curl.cwl

Branch/Commit ID: master