Explore Workflows

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

Graph	Name	Retrieved From	View
	scatter-valuefrom-wf3.cwl#main	https://github.com/common-workflow-language/cwltool.git Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl Branch/Commit ID: 10492acee927c177933160f6ad67085f9112b0d1 Packed ID: main
	tmb_workflow.cwl Workflow to run the TMB analysis on a batch of samples and merge the results back into a single data clinical file	https://github.com/mskcc/pluto-cwl.git Path: cwl/tmb_workflow.cwl Branch/Commit ID: 9f7b5b5f985727a2df34ae86586c296ce757004c
	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: 9f7b5b5f985727a2df34ae86586c296ce757004c
	directory.cwl Inspect provided directory and return filenames. Generate a new directory and return it (including content).	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/directory.cwl Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9
	wgs alignment and somatic variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/somatic_wgs_nonhuman.cwl Branch/Commit ID: 25eab0390f6866ce491b44c89d9e0435d228ab6f
	CLE gold vcf evaluation workflow	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/vcf_eval_cle_gold.cwl Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea
	trim-rnaseq-se-dutp.cwl Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.	https://github.com/datirium/workflows.git Path: workflows/trim-rnaseq-se-dutp.cwl Branch/Commit ID: db6abb2735f87614b870fca9990d36ea786cbbce
	wgs alignment and germline variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/germline_wgs.cwl Branch/Commit ID: 869b331cfeb9dbd5907498e3eccdebc7c28283e5
	wgs alignment and tumor-only variant detection	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/wgs.cwl Branch/Commit ID: c711498c04d6b8ddf92ddceb6219f074765f7993
	revsort.cwl Reverse the lines in a document, then sort those lines.	https://github.com/common-workflow-language/cwltool.git Path: tests/wf/revsort.cwl Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40