Explore Workflows
View already parsed workflows here or click here to add your own
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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: low-vaf |
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SARS_psm_workflow.cwl
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Path: SARS_psm_workflow.cwl Branch/Commit ID: master |
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tRNA_selection.cwl
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Path: tools/tRNA_selection.cwl Branch/Commit ID: 0fed1c9 |
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scatter-wf4.cwl#main
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Path: tests/scatter-wf4.cwl Branch/Commit ID: main Packed ID: main |
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bacterial_screening.cwl
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Path: vecscreen/bacterial_screening.cwl Branch/Commit ID: test |
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collate_unique_SSU_headers.cwl
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Path: tools/collate_unique_SSU_headers.cwl Branch/Commit ID: master |
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cmsearch-multimodel.cwl
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Path: workflows/cmsearch-multimodel.cwl Branch/Commit ID: c1f8b22 |
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Salmon quantification, FASTQ -> H5AD count matrix
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Path: salmon-rnaseq/steps/salmon-quantification.cwl Branch/Commit ID: c338cd3 |
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rw-distr.cwl
run scatter-gather for rw stage |
Path: stage/rw-distr.cwl Branch/Commit ID: master |
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cmsearch-multimodel.cwl
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Path: workflows/cmsearch-multimodel.cwl Branch/Commit ID: f6b5196 |
