Explore Workflows

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

Graph Name Retrieved From View
workflow graph Salmon quantification, FASTQ -> H5AD count matrix

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: steps/salmon-quantification.cwl

Branch/Commit ID: cee6caf
workflow graph ValidationWorkflowMissing

This is a placeholder for a missing acceptance workflow.

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

Path: workflows/ValidationWorkflowMissing.cwl

Branch/Commit ID: main
workflow graph wf-alignment.cwl

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

Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-alignment.cwl

Branch/Commit ID: master
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: downsample_and_recall
workflow graph Detect Variants workflow for WGS pipeline

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

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: master
workflow graph emep_workflow.cwl

https://github.com/UoMResearchIT/wrf_emep_cwl_linear_workflow.git

Path: workflows/emep_workflow.cwl

Branch/Commit ID: develop
workflow graph basename-fields-test.cwl

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

Path: v1.0/v1.0/basename-fields-test.cwl

Branch/Commit ID: master
workflow graph kfdrc-gatk-haplotypecaller-wf.cwl

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

Path: workflows/kfdrc-gatk-haplotypecaller-wf.cwl

Branch/Commit ID: master
workflow graph pipeline-se-blacklist-removal.cwl

ATAC-seq pipeline - reads: SE - with blacklist removal

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

Path: v1.0/ATAC-seq_pipeline/pipeline-se-blacklist-removal.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