Explore Workflows
View already parsed workflows here or click here to add your own
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bgzip and index VCF
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bgzip_and_index.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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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: 59b69eed7ffefcffd81313ec8ffb84c0d716b933 |
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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: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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Apply filters to VCF file
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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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.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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Subworkflow to allow calling different SV callers which require bam files as inputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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Exome QC workflow
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985 |
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Unaligned bam to sorted, markduped bam
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/align_sort_markdup.cwl Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985 |
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Raw sequence data to BQSR
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/sequence_to_bqsr.cwl Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985 |
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Exome QC workflow
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/qc_exome.cwl Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985 |
