Explore Workflows
View already parsed workflows here or click here to add your own
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infuse_pipeline.cwl
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Path: cwls/infuse_pipeline.cwl Branch/Commit ID: dev |
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Uses Bruker TopSpin to convert a zipped NMR data directory to JCAMP-DX
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Path: cwl/zipped2bruker2jcamp.cwl Branch/Commit ID: main |
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revsort-single-no-docker.cwl
Reverse the lines in a document, then sort those lines. |
Path: input-data/revsort-single-no-docker.cwl Branch/Commit ID: master |
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sc_atac_seq_prep_process_analyze.cwl
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Path: sc_atac_seq_prep_process_analyze.cwl Branch/Commit ID: develop |
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gathered exome alignment and somatic variant detection for cle purpose
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Path: definitions/pipelines/somatic_exome_cle_gathered.cwl Branch/Commit ID: downsample_and_recall |
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basename-fields-test.cwl
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Path: tests/basename-fields-test.cwl Branch/Commit ID: main |
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Detect DoCM variants
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Path: definitions/subworkflows/docm_germline.cwl Branch/Commit ID: master |
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umi molecular alignment workflow
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Path: definitions/subworkflows/molecular_alignment.cwl Branch/Commit ID: low-vaf |
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io-int-default-tool-and-wf.cwl
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Path: tests/io-int-default-tool-and-wf.cwl Branch/Commit ID: main |
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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 |
Path: cwl/facets-workflow.cwl Branch/Commit ID: master |
