Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph Per-chromosome pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph bgzip and index VCF

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8
workflow graph facets-workflow.cwl

Workflow for running Facets-suite on a set of tumor normal pairs This workflow scatters over all the pairs in the input JSON to run all samples in parallel Input JSON format ----------------- { \"pairs\": [ { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal1.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.Normal1.maf\" }, \"pair_id\": \"Tumor1.Normal1\" }, { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal2.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.Normal2.maf\" }, \"pair_id\": \"Tumor2.Normal2\" } ] } Output format ------------- output └── facets-suite ├── Tumor1.Normal1.arm_level.txt ├── Tumor1.Normal1.gene_level.txt ├── Tumor1.Normal1_hisens.ccf.maf ├── Tumor1.Normal1_hisens.rds ├── Tumor1.Normal1_hisens.seg ├── Tumor1.Normal1_purity.rds ├── Tumor1.Normal1_purity.seg ├── Tumor1.Normal1.qc.txt ├── Tumor1.Normal1.snp_pileup.gz ├── Tumor1.Normal1.txt ├── Tumor2.Normal2.arm_level.txt ├── Tumor2.Normal2.gene_level.txt ├── Tumor2.Normal2_hisens.ccf.maf ├── Tumor2.Normal2_hisens.rds ├── Tumor2.Normal2_hisens.seg ├── Tumor2.Normal2_purity.rds ├── Tumor2.Normal2_purity.seg ├── Tumor2.Normal2.qc.txt ├── Tumor2.Normal2.snp_pileup.gz ├── Tumor2.Normal2.txt └── logs ├── success └── failed

https://github.com/mskcc/pluto-cwl.git

Path: cwl/facets-workflow.cwl

Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933