Explore Workflows

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

Graph Name Retrieved From View
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_nonhuman.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: b12ec8c8e832151033b9e6c0a76a3c3df18d45da
workflow graph default-dir5.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: 9f3b9e7b74d5a904b12674dfd1300b56a48c3d33
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 93656ed6582073e434eab168c610625a835dce37
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: 87faba2fff8007ecc95160729b1c7cd0376e46f2
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 10870aefd20469e728969269ff3c54b3b8339a18
workflow graph WGS QC workflow nonhuman

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

Path: definitions/subworkflows/qc_wgs_nonhuman.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
workflow graph 04-quantification-pe-stranded.cwl

RNA-seq 04 quantification

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/04-quantification-pe-stranded.cwl

Branch/Commit ID: ebd63f705d0fde7290e42c8300d5420c25cfbfe3