Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph bact_get_kmer_reference

https://github.com/ncbi/pgap.git

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: b38b0070edf910984f29a4a495b5dfa525b8b305
workflow graph samtools_sort

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/samtools_sort.cwl

Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_apollo2_data_processing/processing/workflow.cwl

Branch/Commit ID: c6077d2756e628f469b446e1584ac8a86582d729
workflow graph 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.

https://github.com/datirium/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 4a5c59829ff8b9f3c843e66e3c675dcd9c689ed5
workflow graph 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

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph downsample unaligned BAM and align

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph variant-calling-pair.cwl

https://github.com/mskcc/argos-cwl.git

Path: modules/pair/variant-calling-pair.cwl

Branch/Commit ID: 54c9e02751dc65607f0e334c0eb1a5e646cc71d6
workflow graph picard_markduplicates

Mark duplicates

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e
workflow graph exome alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph bwa_mem

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/bwa_mem.cwl

Branch/Commit ID: 1a8c6bc41c83476a5496bbaca5c3d870cfd8c21e