Explore Workflows

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

Graph Name Retrieved From View
workflow graph Merge, annotate, and generate a TSV for SVs

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: downsample_and_recall
workflow graph forome_vcf_upload_uri.cwl

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

Path: forome_vcf_upload_uri.cwl

Branch/Commit ID: main
workflow graph exomeseq-gatk4-preprocessing/v2.2.0

Whole Exome Sequence preprocessing using GATK4 - v2.2.0

 https://github.com/bespin-workflows/exomeseq-gatk4.git

Path: exomeseq-gatk4-preprocessing.cwl

Branch/Commit ID: develop
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: low-vaf
workflow graph qiime2 diversity analyses

Alpha and beta diversity analysis from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

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

Path: packed/qiime2-step3-alpha-analysis.cwl

Branch/Commit ID: qiime2-workflow-paired

Packed ID: qiime2-06-alpha-beta-diversity.cwl
workflow graph SetTelescopeShadowingParameters

Derive parameters relevant for shadowing components of the telescopes.

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

Path: workflows/SetTelescopeShadowingParameters.cwl

Branch/Commit ID: main
workflow graph maw.cwl

multiple mzml files, all with the same condition

https://github.com/zmahnoor14/MAW.git

Path: cwl/maw.cwl

Branch/Commit ID: main
workflow graph TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)

https://github.com/mscheremetjew/workflow-is-cwl.git

Path: workflows/TransDecoder-v5-wf-2steps.cwl

Branch/Commit ID: assembly
workflow graph Whole Genome Sequence processing workflow scattered over samples

<p>This is a “real-world” workflow example for processing Next Generation Sequencing (NGS) Whole Genome Sequence (WGS) data.</p> <p>You can learn more and run this workflow yourself by going through the <a href=\"https://doc.arvados.org/main/user/tutorials/wgs-tutorial.html\">Processing Whole Genome Sequences</a> walkthrough in the Arvados user guide.</p> <p>The steps of this workflow include:</p> <ol> <li>Check of fastq quality using FastQC</li> <li>Local alignment using BWA-MEM</li> <li>Variant calling in parallel using GATK Haplotype Caller</li> <li>Generation of an HTML report comparing variants against ClinVar archive</li> </ol> <p>The primary input parameter is the <b>Directory of paired FASTQ files</b>, which should contain paired FASTQ files (suffixed with _1 and _2) to be processed. The workflow scatters over the samples to process them in parallel.</p> <p>The remaining parameters are reference data used by various tools in the pipeline.</p>

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/wgs-processing-wf.cwl

Branch/Commit ID: main
workflow graph pulsar_timing_prototype_workflow.cwl

https://github.com/TMCantwell/pulsar_timing_prototype.git

Path: pulsar_timing_prototype_workflow.cwl

Branch/Commit ID: master