Explore Workflows

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

Graph Name Retrieved From View
workflow graph MACE ChIP-exo peak caller workflow for single-end samples

This workflow execute peak caller and QC from ChIP-exo for single-end samples using MACE

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-exo/peak-caller-MACE-SE.cwl

Branch/Commit ID: master
workflow graph call_variants.cwl

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

Path: workflows/subworkflows/call_variants.cwl

Branch/Commit ID: master
workflow graph EMG pipeline v3.0 (paired end version)

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

Path: workflows/emg-pipeline-v3-paired.cwl

Branch/Commit ID: 3f85843
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.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_nanopore_assembly.cwl

Branch/Commit ID: master
workflow graph Genome conversion and annotation

Workflow for genome annotation from EMBL format

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

Path: cwl/workflows/workflow_sapp_others.cwl

Branch/Commit ID: master
workflow graph schemadef-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: 47435d7bfa0240b799acb8e1e8f6b6f8ce03c53c
workflow graph example_workflow.cwl

Example CWL workflow that uses some advanced features

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

Path: cwl/example_workflow.cwl

Branch/Commit ID: 3bc4fab5503e58521ed0eb9c0d035ac18460dc13
workflow graph exomeseq-gatk4-02-variantdiscovery.cwl

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

Path: subworkflows/exomeseq-gatk4-02-variantdiscovery.cwl

Branch/Commit ID: develop
workflow graph qa_check_subwf.cwl

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

https://github.com/svonworl/oxog-dockstore-tools.git

Path: qa_check_subwf.cwl

Branch/Commit ID: master
workflow graph step-valuefrom2-wf_v1_1.cwl

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

Path: testdata/step-valuefrom2-wf_v1_1.cwl

Branch/Commit ID: 33a706bc6b85f1c2824af05bebe7aae19bcb6597