Explore Workflows
View already parsed workflows here or click here to add your own
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SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination
Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs. |
![]() Path: tools/soupx-subworkflow.cwl Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5 |
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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: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f |
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downsample unaligned BAM and align
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![]() Path: definitions/subworkflows/downsampled_alignment.cwl Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470 |
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variant-calling-pair.cwl
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![]() Path: modules/pair/variant-calling-pair.cwl Branch/Commit ID: 54c9e02751dc65607f0e334c0eb1a5e646cc71d6 |
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picard_markduplicates
Mark duplicates |
![]() Path: structuralvariants/subworkflows/picard_markduplicates.cwl Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e |
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exome alignment and germline variant detection
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![]() Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f |
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bwa_mem
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![]() Path: structuralvariants/subworkflows/bwa_mem.cwl Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e |
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genomics-workspace-cds.cwl
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![]() Path: flow_genomicsWorkspace/genomics-workspace-cds.cwl Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729 |
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cnv_exomedepth
CNV ExomeDepth calling |
![]() Path: structuralvariants/subworkflows/cnv_exome_depth.cwl Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e |
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rnaseq-alignment-quantification
This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator |
![]() Path: workflows/RNA-Seq/rnaseq-alignment-quantification.cwl Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419 |