Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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extract_gencoll_ids
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![]() Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: 7c8eb4d23c3c9859f57421643710c0b6d57b606c |
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Filter single sample sv vcf from paired read callers(Manta/Smoove)
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![]() Path: definitions/subworkflows/sv_paired_read_caller_filter.cwl Branch/Commit ID: 9e5f228bc1a3d0dfe950b5d41d7e4319e834a6d4 |
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bwa_pe.cwl
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![]() Path: workflows/mirnaseq_automation/bwa_pe.cwl Branch/Commit ID: 963f6d502da2c4f152c1654e94008ccf8f6d0db3 |
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Dockstore.cwl
updated description testing 1.9.2 |
![]() Path: Dockstore.cwl Branch/Commit ID: 9bde26076ffce492a1ef8e514d05ebc57053423a |
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somatic_exome: exome alignment and somatic variant detection
somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml |
![]() Path: definitions/pipelines/somatic_exome.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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phase VCF
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![]() Path: definitions/subworkflows/phase_vcf.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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exome alignment and germline variant detection, with optitype for HLA typing
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![]() Path: definitions/pipelines/germline_exome_hla_typing.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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RNA-Seq alignment and transcript/gene abundance workflow
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![]() Path: definitions/pipelines/rnaseq.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
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![]() Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325 |
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Subworkflow that runs cnvkit in single sample mode and returns a vcf file
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![]() Path: definitions/subworkflows/cnvkit_single_sample.cwl Branch/Commit ID: 9e5f228bc1a3d0dfe950b5d41d7e4319e834a6d4 |