Explore Workflows

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

Graph Name Retrieved From View
workflow graph tRNA_selection.cwl

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

Path: tools/tRNA_selection.cwl

Branch/Commit ID: 5dc7c5c
workflow graph wf-alignment.cwl

https://github.com/FarahZKhan/bcbio_test_cwl.git

Path: somatic/somatic-workflow/wf-alignment.cwl

Branch/Commit ID: master
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: master
workflow graph Metagenomics workflow

Workflow for Metagenomics from raw reads to annotated bins. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - SPAdes (Assembly) - QUAST (Assembly quality report) - BBmap (Read mapping to assembly) - Contig binning (OPTIONAL)

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

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: master
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: downsample_and_recall
workflow graph Nanopore Quality Control and Filtering

**Workflow for nanopore read quality control and contamination filtering.** - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 read filtering based on given references - FastQC after filtering (read quality control) **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> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

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

Path: cwl/workflows/workflow_nanopore_quality.cwl

Branch/Commit ID: master
workflow graph bulk scRNA-seq pipeline using Salmon

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

Path: bulk-pipeline.cwl

Branch/Commit ID: 8af5a1c
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 Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: downsample_and_recall
workflow graph exome alignment and tumor-only variant detection

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

Path: definitions/pipelines/tumor_only_exome.cwl

Branch/Commit ID: downsample_and_recall