Explore Workflows

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

Graph Name Retrieved From View
workflow graph Cell Ranger ARC Aggregate

Cell Ranger ARC Aggregate =========================

https://github.com/datirium/workflows.git

Path: workflows/cellranger-arc-aggr.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9
workflow graph cond-wf-012_nojs.cwl

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

Path: tests/conditionals/cond-wf-012_nojs.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735
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: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph allele-process-strain.cwl

https://github.com/datirium/workflows.git

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf
workflow graph analysis-workflow.cwl

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

Path: cwl/analysis-workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77
workflow graph allele-process-reference.cwl

https://github.com/datirium/workflows.git

Path: subworkflows/allele-process-reference.cwl

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf
workflow graph example.cwl

Example CWL workflow that uses some advanced features

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

Path: cwl/example.cwl

Branch/Commit ID: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e
workflow graph allele-rnaseq-se.cwl

Allele specific RNA-Seq single-read workflow

https://github.com/datirium/workflows.git

Path: workflows/allele-rnaseq-se.cwl

Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf