Explore Workflows

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

Graph Name Retrieved From View
workflow graph dedup-2-pass.cwl

run 2-pass dedup: algo LocusCollector + algo Dedup sequentially

 https://github.com/sentieon/sentieon-cwl.git

Path: stage/dedup-2-pass.cwl

Branch/Commit ID: d20382adfe7285cb517a25d95d2bcb7586546e23
workflow graph Nanopore Quality Control and Filtering

**Workflow for nanopore read quality control and contamination filtering.** - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 read filtering based on given references - FastQC after filtering (read quality control) **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> WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

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

Path: cwl/workflows/workflow_nanopore_quality.cwl

Branch/Commit ID: master
workflow graph Quality assessment, amplicon classification and functional prediction

Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. 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 - Picrust 2 - Export module for ngtax

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

Path: cwl/workflows/workflow_ngtax_picrust2.cwl

Branch/Commit ID: master
workflow graph SAMSA2 pipeline

SAMSA2 complete workflow for meta-omics read annotation Steps: - Diamond read blastx - Refseq - SEED - SAMSA2 processing

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

Path: cwl/workflows/workflow_samsa2.cwl

Branch/Commit ID: master
workflow graph workflow_mock_ngtax.cwl

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

Path: cwl/workflows/workflow_mock_ngtax.cwl

Branch/Commit ID: master
workflow graph Conversion and compression of RDF files

Workflow to convert a RDF file to the HDT format and GZIP compress it for long term storage

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

Path: cwl/workflows/workflow_toHDT_compression.cwl

Branch/Commit ID: master
workflow graph CroMaSt.cwl

https://gitlab.inria.fr/capsid.public_codes/CroMaSt.git

Path: CroMaSt.cwl

Branch/Commit ID: b5a9d4b025ec8e065bae97eeb96f10db2dd8e1e6
workflow graph umi per-lane alignment subworkflow

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

Path: definitions/subworkflows/umi_alignment.cwl

Branch/Commit ID: e649fcb1092905c539be026a3f23c82d5b0871d2
workflow graph Whole Exome Sequencing

Whole Exome Sequence analysis using GATK best practices - Germline SNP & Indel Discovery

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

Path: packed/exomeseq.cwl

Branch/Commit ID: e2dc95d4f12210359360d814382e7201d836dfcf

Packed ID: main
workflow graph Metagenomics workflow

Workflow pilon assembly polishing Steps: - BBmap (Read mapping to assembly) - Pilon

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

Path: cwl/workflows/workflow_pilon_mapping.cwl

Branch/Commit ID: master