Explore Workflows
View already parsed workflows here or click here to add your own
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Unaligned BAM to BQSR and VCF
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bam_to_bqsr_no_dup_marking.cwl Branch/Commit ID: 86fbeb95ef85111f3b4c6bc2bba8f06cef64e157 |
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exome alignment and germline variant detection, with optitype for HLA typing
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/germline_exome_hla_typing.cwl Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511 |
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count-lines4-wf.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl Branch/Commit ID: 639229b1159cf484e70e52da10194561b3fad719 |
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cond-wf-004.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/conditionals/cond-wf-004.cwl Branch/Commit ID: 979083396fee912fca8ef778174216d317338a00 |
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count-lines9-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/count-lines9-wf.cwl Branch/Commit ID: 979083396fee912fca8ef778174216d317338a00 |
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count-lines11-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/count-lines11-wf.cwl Branch/Commit ID: 979083396fee912fca8ef778174216d317338a00 |
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count-lines15-wf.cwl
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https://github.com/common-workflow-language/cwl-v1.2.git
Path: tests/count-lines15-wf.cwl Branch/Commit ID: 979083396fee912fca8ef778174216d317338a00 |
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js_output_workflow.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/js_output_workflow.cwl Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b |
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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: e19ef998e906eb915cf4351a3599abd9bff57205 |
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811.cwl
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/811.cwl Branch/Commit ID: 955616b6c7692465bd85f6eb3e0e1cd2672124f4 |
