Explore Workflows

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Graph Name Retrieved From View
workflow graph trimmed_fastq

Quality Control (raw data), Raw Data trimming and Quality Control (pre-processed)

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

Path: structuralvariants/cwl/abstract_operations/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: aaecc710f76be9285288a975cc786e354bc9bedf

workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 5282690e0f634a5f83107ba878fe62cbbb347408

workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d

workflow graph samtools_sort

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

Path: structuralvariants/cwl/subworkflows/samtools_sort.cwl

Branch/Commit ID: 6ccec9c5c5bc9fb4e75ca0b9cc22d13df9ffb815

workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370

workflow graph tmb.cwl

Workflow for calculating TMB tumor mutational burden on a single sample

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

Path: cwl/tmb.cwl

Branch/Commit ID: 45604eaeea15030c7302941c761464ce392abf74

workflow graph bacterial_kmer

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3

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: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370

workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: 505b91e41741ccbcd5ebd2b6a09a3be604f9ece3

workflow graph tt_kmer_compare_wnode

Pairwise comparison

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

Path: task_types/tt_kmer_compare_wnode.cwl

Branch/Commit ID: 8fb4ac7f5a66897206c7469101a471108b06eada