Explore Workflows

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

Graph Name Retrieved From View
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 EMG assembly for paired end Illumina

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

Path: workflows/emg-pipeline-v4-assembly-metaSPAdes.cwl

Branch/Commit ID: master
workflow graph picard_markduplicates

Mark duplicates

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 1.0.7
workflow graph workflow_data.cwl

https://github.com/mr-c/cwltests.git

Path: cwl/workflow_data.cwl

Branch/Commit ID: pack_test
workflow graph testTimeSIMLR.cwl

https://github.com/Gepiro/rCASCStreamFlow.git

Path: setting/testTimeSIMLR.cwl

Branch/Commit ID: main
workflow graph call_variants.cwl

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

Path: workflows/subworkflows/call_variants.cwl

Branch/Commit ID: master
workflow graph wf_trim_and_map_se_nostats.cwl

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/YeoLab/eclip.git

Path: cwl/wf_trim_and_map_se_nostats.cwl

Branch/Commit ID: master
workflow graph cond-wf-003.1.cwl

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

Path: testdata/cond-wf-003.1.cwl

Branch/Commit ID: main
workflow graph ST520115.cwl

https://github.com/Marco-Salvi/cwl-test.git

Path: wf5201/ST520115.cwl

Branch/Commit ID: main
workflow graph extract_file_with_index.cwl

https://github.com/NCI-GDC/aliquot-maf-cwl.git

Path: vcf-to-aliquot-maf/subworkflows/extract_file_with_index.cwl

Branch/Commit ID: main