Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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workflow.cwl
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https://github.com/FarahZKhan/scalability-reproducibility-chapter.git
Path: CWL/workflow.cwl Branch/Commit ID: ProvCaptureDemo |
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03-map-se-blacklist-removal.cwl
ATAC-seq 03 mapping - reads: SE |
https://github.com/alexbarrera/GGR-cwl.git
Path: v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl Branch/Commit ID: v1.0 |
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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 |
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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 |
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collate_unique_SSU_headers.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: tools/collate_unique_SSU_headers.cwl Branch/Commit ID: 1b0851e |
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exomeseq.cwl#exomeseq-02-variantdiscovery.cwl
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https://github.com/Duke-GCB/bespin-cwl.git
Path: packed/exomeseq.cwl Branch/Commit ID: qiime2-workflow-paired Packed ID: exomeseq-02-variantdiscovery.cwl |
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EMG core analysis
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https://github.com/proteinswebteam/ebi-metagenomics-cwl.git
Path: workflows/emg-core-analysis-v4.cwl Branch/Commit ID: master |
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wf.cwl#SplitAndSubsample.cwl
SplitAndSubsample splits, subsamples and formats read files to be deposited in QualityFilter. |
https://github.com/aheinzel/tmp_rhapsody_for_cwl_vis.git
Path: wf.cwl Branch/Commit ID: main Packed ID: SplitAndSubsample.cwl |
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SPRM pipeline
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https://github.com/hubmapconsortium/sprm.git
Path: pipeline.cwl Branch/Commit ID: 62d3a80 |
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chksum_for_a_corrupted_fastq_file.cwl
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https://github.com/cancerit/workflow-seq-import.git
Path: cwls/chksum_for_a_corrupted_fastq_file.cwl Branch/Commit ID: develop |
