Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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freebayes.cwl
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https://github.com/uc-cdis/genomel_pipelines.git
Path: genomel/cwl/workflows/variant_calling/freebayes.cwl Branch/Commit ID: 7f01768479e6a77a5caf6b3382174aa038ba05fc |
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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: 7eb2b0a4d37018142233d770595ac2e00376dab4 |
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scatter-wf4.cwl#main
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https://github.com/common-workflow-language/cwltool.git
Path: tests/wf/scatter-wf4.cwl Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda Packed ID: main |
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align_merge_sas
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https://github.com/ncbi/pgap.git
Path: task_types/tt_align_merge_sas.cwl Branch/Commit ID: e3f18c61d1bbf65e40921dbd044369da4523ee3e |
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readme-assembly-workflow.cwl
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https://github.com/nal-i5k/organism_onboarding.git
Path: flow_create_readme/readme-assembly-workflow.cwl Branch/Commit ID: 89cff9f0d36a23bf57b3f4bdbd3ed57e3347c945 |
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Varscan Workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/varscan_germline.cwl Branch/Commit ID: a08de598edc04f340fdbff76c9a92336a7702022 |
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samples_fillout_workflow.cwl
Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files |
https://github.com/mskcc/pluto-cwl.git
Path: cwl/samples_fillout_workflow.cwl Branch/Commit ID: 7eb2b0a4d37018142233d770595ac2e00376dab4 |
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tt_kmer_top_n.cwl
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https://github.com/ncbi/pgap.git
Path: task_types/tt_kmer_top_n.cwl Branch/Commit ID: 369afa7090a7480e6a0b144eff967a4a52b6fde2 |
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cache_asnb_entries
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https://github.com/ncbi/pgap.git
Path: task_types/tt_cache_asnb_entries.cwl Branch/Commit ID: d39017c63dd8e088f1ad3809d709529df602e05f |
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Single-Cell Preprocessing Cell Ranger Pipeline
Devel version of Single-Cell Preprocessing Cell Ranger Pipeline =============================================================== |
https://github.com/datirium/workflows.git
Path: workflows/single-cell-preprocess-cellranger.cwl Branch/Commit ID: 7fb8a1ebf8145791440bc2fed9c5f2d78a19d04c |
