Explore Workflows

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

Graph Name Retrieved From View
workflow graph bwameth_mulitlib.cwl

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

Path: CWL/workflows/bwameth/bwameth_mulitlib.cwl

Branch/Commit ID: main
workflow graph realignment.cwl

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/realignment.cwl

Branch/Commit ID: 507efdf727d2a5ec7b91007e7c953b1a2d81b288
workflow graph Functional analyis of sequences that match the 16S SSU

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

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: ca6ca613
workflow graph Detect Variants workflow

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

Path: detect_variants/detect_variants.cwl

Branch/Commit ID: toil_compatibility
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: cwlprov_testing
workflow graph cmsearch-multimodel.cwl

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

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: a8abd0e
workflow graph exomeseq-gatk4-03-organizedirectories.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-gatk4-03-organizedirectories.cwl

Branch/Commit ID: gatk4-fixes
workflow graph main-giab-chm.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: giab-chm/giab-chm-workflow/main-giab-chm.cwl

Branch/Commit ID: master
workflow graph Exome QC workflow

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: low-vaf
workflow graph Transcripts annotation workflow

https://github.com/mr-c/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-wf.cwl

Branch/Commit ID: fix_sbg_namespace