Explore Workflows

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: annotator_sub_wf.cwl

Branch/Commit ID: 6366ed398da10019b6d81a789291af6d909f28f4

https://github.com/4dn-dcic/pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-parta-juicer.cwl

Branch/Commit ID: 91d67820264c8ebac829174cb1d0c7c5e30c613f

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 583307878ab83c5845c897f03db920ae8e1929e2

This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output.

https://github.com/ICGC-TCGA-PanCancer/pcawg-oxog-filter.git

Path: zip_and_index_vcf.cwl

Branch/Commit ID: 123a3151d35f98e442e703d903dc3e1d72f3c4b0

https://github.com/Epigenomics-Screw/Screw.git

Path: cwl/preprocess.cwl

Branch/Commit ID: eca4d48b08fef0a81518ce3441ed47fcfff412a6

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/dnaseq/mixed_library_metrics.cwl

Branch/Commit ID: d5757ab1f3aad3c542950e1dbe8f9d2eec74bede

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 3f85843d4a6debdabe96bc800bf2a4efdcda1ef3

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

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

Path: preprocess_vcf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3

https://github.com/KBNLresearch/ochre.git

Path: ochre/cwl/sac-preprocess.cwl

Branch/Commit ID: bfd504ae910fbf7a3492f53430a1c9f3c3c97470

Packed ID: main

https://github.com/bcbio/bcbio_validation_workflows.git

Path: somatic-giab-mix/somatic-giab-mix-workflow/wf-variantcall.cwl

Branch/Commit ID: c4592973b1580e3ff44cb697f64b12345b91e6f5