Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-valuefrom-wf5.cwl

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

Path: v1.0/v1.0/scatter-valuefrom-wf5.cwl

Branch/Commit ID: master
workflow graph harmonization_bwa_mem_no_trim.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/harmonization_bwa_mem_no_trim.cwl

Branch/Commit ID: master
workflow graph vardictSomaticVariantCaller_v0_1_0.cwl

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

Path: janis_pipelines/wgs_somatic/cwl/tools/vardictSomaticVariantCaller_v0_1_0.cwl

Branch/Commit ID: master
workflow graph post-proccessing-go-pfam-stats-subwf.cwl

https://github.com/kinow/pipeline-v5.git

Path: workflows/subworkflows/functional-annotation/post-proccessing-go-pfam-stats-subwf.cwl

Branch/Commit ID: eosc-life-gos
workflow graph standard_pipeline.cwl

This is a workflow to go from UMI-tagged fastqs to standard bams. It does not include collapsing, or QC It does include modules 1 and 2

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/standard_pipeline.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: cwlprov_testing
workflow graph kfdrc_sentieon_gvcf_wf.cwl

https://github.com/kids-first/kf-alignment-workflow.git

Path: workflows/kfdrc_sentieon_gvcf_wf.cwl

Branch/Commit ID: master
workflow graph snps_and_indels.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/subworkflows/snps_and_indels.cwl

Branch/Commit ID: master
workflow graph ocrevaluation-performance-wf-pack.cwl#main

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

Path: ochre/cwl/ocrevaluation-performance-wf-pack.cwl

Branch/Commit ID: master

Packed ID: main
workflow graph snp_callers_workflow.cwl

A workflow for running MuSe, MuTect, SomaticSniper, and Pindel. See [the github repository](https://github.com/BD2KGenomics/dockstore_workflow_snps) for details.

https://github.com/bd2kgenomics/dockstore_workflow_snps.git

Path: snp_callers_workflow.cwl

Branch/Commit ID: master