Explore Workflows

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

Path: oxog_varbam_annotate_wf.cwl

Branch/Commit ID: master

https://github.com/Aeolic/example-workflow.git

Path: example_workflow.cwl

Branch/Commit ID: main

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

Path: tests/io-int-optional-wf.cwl

Branch/Commit ID: main

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

Path: structuralvariants/cwl/subworkflows/indexing_bed.cwl

Branch/Commit ID: 1.0.5

https://github.com/common-workflow-language/common-workflow-language.git

Path: v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: master

Compute average structure for all averaged structures corresponding to UniProt domain instances cross-mapped from Pfam/CATH to a CATH/Pfam family. First computes average per UniProt domain instance and then average all averaged structures per Pfam family.

https://github.com/HrishiDhondge/CroMaSt.git

Path: Tools/other_avg_subwf.cwl

Branch/Commit ID: main

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

Path: tests/iwdr_with_nested_dirs.cwl

Branch/Commit ID: master

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: master

This subworkflow will perform a QA check on the OxoG outputs. It will perform the QA check on a single tumour and it associated VCFs

https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: qa_check_subwf.cwl

Branch/Commit ID: master

Water body detection based on NDWI and otsu threshold

https://github.com/Terradue/ogc-eo-application-package-hands-on.git

Path: water-bodies/app-package.cwl

Branch/Commit ID: bids23

Packed ID: detect_water_body