Explore Workflows

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

Graph Name Retrieved From View
workflow graph module-6

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-6.cwl

Branch/Commit ID: 2.4.x
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: master

Packed ID: main
workflow graph scRNA-seq pipeline using Salmon and Alevin

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

Path: pipeline.cwl

Branch/Commit ID: cee6caf
workflow graph qiime2 Deblur detect/correct sequence data

Option 2: Deblur from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step2-deblur.cwl

Branch/Commit ID: qiime2-workflow-paired

Packed ID: qiime2-03-deblur.cwl
workflow graph trimming-and-qc-no-upload.cwl

Use fastq file as input and do trimming and quality check. Quality checks are done before trimming and after trimming.

 https://github.com/ddbj/SAPPORO_test_workflow.git

Path: workflow/trimming-and-qc/trimming-and-qc-no-upload/trimming-and-qc-no-upload.cwl

Branch/Commit ID: master
workflow graph qiime2 explore sample taxonomic composition

Taxonomic analysis from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

 https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: qiime2-08-taxonomic-analysis.cwl
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 collate_unique_SSU_headers.cwl

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

Path: tools/collate_unique_SSU_headers.cwl

Branch/Commit ID: 5dc7c5c
workflow graph Unaligned BAM to BQSR and VCF

https://github.com/markrobbo/workflows.git

Path: workflows/hello/exome_alignment_packed.cwl

Branch/Commit ID: master

Packed ID: workflow.cwl_2
workflow graph md5sum-workflow.cwl

https://github.com/fhembroff/md5sum-checker.git

Path: md5sum/md5sum-workflow.cwl

Branch/Commit ID: master