Explore Workflows

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

Graph Name Retrieved From View
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.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_nanopore_quality.cwl

Branch/Commit ID: 2242521957bb07fc589d6bb07046f6a166bc975a
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

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

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f
workflow graph extract_gencoll_ids

https://github.com/ncbi/pgap.git

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 90a321ecf2d049330bcf0657cc4d764d2c3f42dd
workflow graph Metagenomics workflow

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

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

Path: cwl/workflows/workflow_pilon_mapping.cwl

Branch/Commit ID: 2242521957bb07fc589d6bb07046f6a166bc975a
workflow graph kmer_cache_retrieve

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 4def84df33963fc9ac9d5c5f804b911d01a0d9ad
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: cbefc215d8286447620664fb47076ba5d81aa47f
workflow graph echo-wf-default.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/echo-wf-default.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph import_schema-def.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/import_schema-def.cwl

Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
workflow graph tt_kmer_compare_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: f6950321e5c9ee733ad68a273d2ad8e802a6b982
workflow graph Cell Ranger ARC Aggregate

Cell Ranger ARC Aggregate =========================

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

Path: workflows/cellranger-arc-aggr.cwl

Branch/Commit ID: 60854b5d299df91e135e05d02f4be61f6a310fbc