Explore Workflows

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/ICGC-TCGA-PanCancer/pcawg-snv-indel-annotation.git

Path: preprocess_vcf.cwl

Branch/Commit ID: develop

https://github.com/stevetsa/Metaphlan-ISBCGC.git

Path: metaphlan_wfl.cwl

Branch/Commit ID: master

https://github.com/ChrisMaherLab/PACT.git

Path: subworkflows/fp_filter.cwl

Branch/Commit ID: master

This workflow detect and remove foreign chromosome from a DNA fasta file

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

Path: workflows/Contamination/contamination-foreign-chromosome-blastn.cwl

Branch/Commit ID: master

https://github.com/kathy-t/ghapps-single-workflow.git

Path: Dockstore.cwl

Branch/Commit ID: annotated-tag-3

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

Path: tests/count-lines6-wf.cwl

Branch/Commit ID: main

https://github.com/hamid58b/cancer-genomics-workflow.git

Path: varscan/workflow.cwl

Branch/Commit ID: master

https://gitlab.com/unduthegun/stellaris-emblem-lab.git

Path: textures/emblem_textures.cwl

Branch/Commit ID: master

Create emblem textures

https://github.com/undu/stellaris-emblem-lab.git

Path: textures/textures.cwl

Branch/Commit ID: cwl

Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/subworkflows/find_hotspots_in_normals.cwl

Branch/Commit ID: master