Explore Workflows

**VCF to GDS** workflow converts VCF or BCF files into Genomic Data Structure (GDS) format. GDS files are required by all workflows utilizing the GENESIS or SNPRelate R packages. _Filename requirements_: The input file names should follow the pattern <A>chr<X>.<y> For example: 1KG_phase3_subset_chr1.vcf.gz Some of the tools inside the workflow infer the chromosome number from the file by expecting this pattern of file name.

https://github.com/sevenbridges-openworkflows/uw-genesis-topmed-cwl.git

Path: vcftogds/vcf-to-gds-wf.cwl

Branch/Commit ID: master

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/BwaAligner_1_0_0.cwl

Branch/Commit ID: master

Description of checker workflow here

https://github.com/denis-yuen/dockstore-workflow-md5sum-unified.git

Path: checker_workflow.cwl

Branch/Commit ID: 1.3.0

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-fasta-pratt.cwl

Branch/Commit ID: master

Mark duplicates

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

Path: structuralvariants/cwl/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 1.0.7

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/yyoshiaki/VIRTUS2.git

Path: workflow/VIRTUS.SE.cwl

Branch/Commit ID: master

https://github.com/andurill/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow.cwl

Branch/Commit ID: master

https://github.com/lanl/BEE.git

Path: examples/cat-grep-tar/workflow.cwl

Branch/Commit ID: develop

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

Path: tests/scatter-wf1.cwl

Branch/Commit ID: main