Explore Workflows

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

Graph Name Retrieved From View
workflow graph Find reads with predicted coding sequences above 60 AA in length

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

Path: workflows/orf_prediction.cwl

Branch/Commit ID: master
workflow graph count-lines8-wf-noET.cwl

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

Path: v1.0/v1.0/count-lines8-wf-noET.cwl

Branch/Commit ID: master
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 module-4.cwl

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

Path: workflows/module-4.cwl

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

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/step-valuefrom2-wf.cwl

Branch/Commit ID: master
workflow graph EMG core analysis

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

Path: workflows/emg-core-analysis-v4.cwl

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

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

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: ca6ca613
workflow graph wf-variantcall.cwl

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

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

Branch/Commit ID: master
workflow graph 02-trim-pe.cwl

STARR-seq 02 trimming - reads: PE

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

Path: v1.0/STARR-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: master
workflow graph gatk-4.0.0.0-joint-calling.cwl

https://github.com/wtsi-hgi/arvados-pipelines.git

Path: cwl/workflows/gatk-4.0.0.0-joint-calling.cwl

Branch/Commit ID: master