Explore Workflows

**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

https://github.com/EBI-Metagenomics/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-i5only-wf.cwl

Branch/Commit ID: assembly

https://github.com/hubmapconsortium/codex-pipeline.git

Path: steps/ometiff_second_stitching.cwl

Branch/Commit ID: cf68e50

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/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: oxog_sub_wf.cwl

Branch/Commit ID: master

https://github.com/kids-first/kf-rnaseq-workflow.git

Path: workflow/rmats_wf.cwl

Branch/Commit ID: master

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/dnaseq/runner.cwl

Branch/Commit ID: 1.1

https://github.com/kyusque/abmp_log_dump2pieda.git

Path: test-data2.cwl

Branch/Commit ID: master

https://github.com/as595/cwl_rmsynth.git

Path: rmsynth_workflow1.cwl

Branch/Commit ID: master

https://github.com/jarnolaitinen/RD_pipeline.git

Path: workflow_localfiles.cwl

Branch/Commit ID: master

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: test