Explore Workflows
View already parsed workflows here or click here to add your own
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Running cellranger count and lineage inference
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_cell_rnaseq.cwl Branch/Commit ID: efbbe5ed51f6ac583e87a348785c72818a33f56e |
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Seurat Cluster
Seurat Cluster ============== Runs filtering, integration, and clustering analyses for Cell Ranger Count Gene Expression or Cell Ranger Aggregate experiments. |
https://github.com/datirium/workflows.git
Path: workflows/seurat-cluster.cwl Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9 |
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output-arrays-int-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/output-arrays-int-wf.cwl Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b |
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conflict-wf.cwl#collision
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl Branch/Commit ID: ec2cf2da6c31ffedf827a0fb213b5204e172f510 Packed ID: collision |
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running cellranger mkfastq and count
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3 |
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Cell Ranger ARC Aggregate
Cell Ranger ARC Aggregate ========================= |
https://github.com/datirium/workflows.git
Path: workflows/cellranger-arc-aggr.cwl Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9 |
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cond-wf-012_nojs.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/conditionals/cond-wf-012_nojs.cwl Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733 |
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WGS QC workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/qc_wgs.cwl Branch/Commit ID: f9600f9959acdc30259ba7e64de61104c9b01f0b |
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Detect Variants workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/detect_variants.cwl Branch/Commit ID: 27dcb1ae121be6a23057b74332b8c752ea425735 |
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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 |
