Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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trimmed_fastq
Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed) |
![]() Path: structuralvariants/cwl/abstract_operations/subworkflows/trimmed_fastq.cwl Branch/Commit ID: aaecc710f76be9285288a975cc786e354bc9bedf |
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assm_assm_blastn_wnode
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![]() Path: task_types/tt_assm_assm_blastn_wnode.cwl Branch/Commit ID: 5282690e0f634a5f83107ba878fe62cbbb347408 |
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phase VCF
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![]() Path: definitions/subworkflows/phase_vcf.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
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samtools_sort
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![]() Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl Branch/Commit ID: 6ccec9c5c5bc9fb4e75ca0b9cc22d13df9ffb815 |
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Varscan Workflow
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![]() Path: definitions/subworkflows/varscan_germline.cwl Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370 |
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tmb.cwl
Workflow for calculating TMB tumor mutational burden on a single sample |
![]() Path: cwl/tmb.cwl Branch/Commit ID: 45604eaeea15030c7302941c761464ce392abf74 |
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bacterial_kmer
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![]() Path: bacterial_kmer/wf_bacterial_kmer.cwl Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3 |
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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: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370 |
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taxcheck.cwl
Perform taxonomic identification tasks on an input genome |
![]() Path: taxcheck.cwl Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3 |
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tt_kmer_compare_wnode
Pairwise comparison |
![]() Path: task_types/tt_kmer_compare_wnode.cwl Branch/Commit ID: 8fb4ac7f5a66897206c7469101a471108b06eada |