Explore Workflows

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

Graph Name Retrieved From View
workflow graph Chunked version of phmmer-v3.2.cwl

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

Path: workflows/phmmer-v3.2-chunked-wf.cwl

Branch/Commit ID: master
workflow graph workflow.cwl

https://github.com/lonbar/workflow.git

Path: workflow.cwl

Branch/Commit ID: main
workflow graph trimming-and-qc-no-upload.cwl

Use fastq file as input and do trimming and quality check. Quality checks are done before trimming and after trimming.

 https://github.com/ddbj/SAPPORO_test_workflow.git

Path: workflow/trimming-and-qc/trimming-and-qc-no-upload/trimming-and-qc-no-upload.cwl

Branch/Commit ID: master
workflow graph sample-workflow.cwl

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

Path: workflows/sample-workflow.cwl

Branch/Commit ID: master
workflow graph checker_workflow_wrapping_tool.cwl

This demonstrates how to wrap a \"real\" tool with a checker workflow that runs both the tool and a tool that performs verification of results

https://github.com/dockstore-testing/dockstore-workflow-md5sum-unified.git

Path: checker_workflow_wrapping_tool.cwl

Branch/Commit ID: 1.3.0
workflow graph consensus_bed.cwl

Workflow to merge a large number of maf files into a single consensus bed file

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

Path: cwl/consensus_bed.cwl

Branch/Commit ID: master
workflow graph module-1

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-1.cwl

Branch/Commit ID: dev
workflow graph Nanopore assembly workflow

**Workflow for sequencing with ONT Nanopore data, from basecalled reads to (meta)assembly and binning**<br> - Workflow Nanopore Quality - Kraken2 taxonomic classification of FASTQ reads - Flye (de-novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) **When Illumina reads are provided:** - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - Assembly polishing with Pilon<br> - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2 - CheckM - BUSCO - GTDB-Tk **All tool CWL files and other workflows can be found here:**<br> Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl<br> Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows<br> The dependencies are either accessible from https://unlock-icat.irods.surfsara.nl (anonymous,anonymous)<br> and/or<br> By using the conda / pip environments as shown in https://git.wur.nl/unlock/docker/-/blob/master/kubernetes/scripts/setup.sh<br>

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_nanopore_assembly.cwl

Branch/Commit ID: master
workflow graph BlastP_RBH_workflow

https://github.com/ncbi/cwl-demos.git

Path: blast-pipelines/blast_workflow.cwl

Branch/Commit ID: master
workflow graph minibam_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/icgc-tcga-pancancer/oxog-dockstore-tools.git

Path: minibam_sub_wf.cwl

Branch/Commit ID: 1.0.0