Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cell Ranger Build Reference Indices

Devel version of Cell Ranger Build Reference Indices pipeline =============================================================

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

Path: workflows/cellranger-mkref.cwl

Branch/Commit ID: 954bb2f213d97dfef1cddaf9e830169a92ad0c6b
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Whole_Exome-Seq.cwl

https://github.com/athenarc/whole-exome-seq.git

Path: workflows/Whole_Exome-Seq.cwl

Branch/Commit ID: de6ee08d2ff7621c3e07e70881624f342da8b826
workflow graph fastq2fasta.cwl

https://github.com/arvados/bh20-seq-resource.git

Path: workflows/fastq2fasta/fastq2fasta.cwl

Branch/Commit ID: 2ae71911cd87ce4f2eabdff21e538267b3270d45
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: b9097b82e6ab6f2c9496013ce4dd6877092956a0
workflow graph Dockstore.cwl

https://github.com/kathy-t/ghapps-single-workflow.git

Path: Dockstore.cwl

Branch/Commit ID: d39c5b5a0939eaa544bb200afe94d75ecddac405
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph tmb_workflow.cwl

Workflow to run the TMB analysis on a batch of samples and merge the results back into a single data clinical file

https://github.com/mskcc/pluto-cwl.git

Path: cwl/tmb_workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph ribosomal_cleanup

This workflow detect and remove ribosomal from a DNA fasta file

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Contamination/ribosomal-cleanup.cwl

Branch/Commit ID: 1b1cb5bbbe53a2dd5d7de7cdbff19c1bdbe23a49