Explore Workflows

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

Graph Name Retrieved From View
workflow graph (Hybrid) Metagenomics workflow

**Workflow (hybrid) metagenomic assembly and binning **<br> - Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1 - FastQC (control) - fastp (quality trimming) - kraken2 (taxonomy) - bbmap contamination filter - Kraken2 taxonomic classification of FASTQ reads - SPAdes/Flye (Assembly) - QUAST (Assembly quality report) (optional) - Workflow binnning https://workflowhub.eu/workflows/64?version=11 - Metabat2/MaxBin2/SemiBin - DAS Tool - CheckM - BUSCO - GTDB-Tk (optional) - Workflow Genome-scale metabolic models https://workflowhub.eu/workflows/372 - CarveMe (GEM generation) - MEMOTE (GEM test suite) - SMETANA (Species METabolic interaction ANAlysis) Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default<br><br> **All tool CWL files and other workflows can be found here:**<br> Tools: https://gitlab.com/m-unlock/cwl<br> Workflows: https://gitlab.com/m-unlock/cwl/workflows<br> **How to setup and use an UNLOCK workflow:**<br> https://m-unlock.gitlab.io/docs/setup/setup.html<br>

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_assembly.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503
workflow graph scatter-wf4.cwl#main

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-wf4.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

Packed ID: main
workflow graph oxog_varbam_annotate_wf.cwl

This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json `

https://github.com/svonworl/oxog-dockstore-tools.git

Path: oxog_varbam_annotate_wf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3
workflow graph annotator_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/svonworl/oxog-dockstore-tools.git

Path: annotator_sub_wf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3
workflow graph minibam_sub_wf.cwl

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/svonworl/oxog-dockstore-tools.git

Path: minibam_sub_wf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3
workflow graph Quality assessment, amplicon classification

Workflow for quality assessment of paired reads and classification using NGTax 2.0. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps: - FastQC (read quality control) - NGTax 2.0 - Export module

https://git.wageningenur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_ngtax.cwl

Branch/Commit ID: b9097b82e6ab6f2c9496013ce4dd6877092956a0
workflow graph Metagenomic GEM construction from assembly

Workflow for Metagenomics from bins to metabolic model.<br> Summary - Prodigal gene prediction - CarveMe genome scale metabolic model reconstruction - MEMOTE for metabolic model testing - SMETANA Species METabolic interaction ANAlysis Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default<br><br> **All tool CWL files and other workflows can be found here:**<br> Tools: https://gitlab.com/m-unlock/cwl<br> Workflows: https://gitlab.com/m-unlock/cwl/workflows<br> **How to setup and use an UNLOCK workflow:**<br> https://m-unlock.gitlab.io/docs/setup/setup.html<br>

https://gitlab.com/m-unlock/cwl.git

Path: cwl/workflows/workflow_metagenomics_GEM.cwl

Branch/Commit ID: 50aaa5a89d0cd01c80d55fb68dd72708d3796503
workflow graph CNV_pipeline

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

Path: structuralvariants/cwl/workflow.cwl

Branch/Commit ID: 94bcf49c6f22055a359336d2e593f8289f1c5e48
workflow graph contaminant_cleanup

This workflow detect and remove contamination from a DNA fasta file

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

Path: workflows/Contamination/contaminant-cleanup.cwl

Branch/Commit ID: e1c19e64f6fc210f65472ee227786d33c9b4909a
workflow graph DESeq2 Multi-factor Analysis

DESeq2 Multi-factor Analysis ============================ Runs DeSeq2 multi-factor analysis with manual control over major parameters

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

Path: workflows/deseq-multi-factor.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5