Explore Workflows

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

Graph Name Retrieved From View
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: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/alignment_exome_mouse.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 8438316338e66823e1c9aca9f675b2bf33f2aa59
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 77a9fa25b89ce73582a1ce6ba75fa6d2537fb8e8
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 546742b523ce12f6246a52c838a51920a08dad4b
workflow graph wf_full_IDR_pipeline_2inputs.cwl

The main workflow that: produces two reproducible peaks via IDR given two eCLIP samples (1 input, 1 IP each). runs the 'rescue ratio' statistic runs the 'consistency ratio' statistic

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_full_IDR_pipeline_2inputs.cwl

Branch/Commit ID: 18933d4d4b00e97a8a0d155abbebad1fdbc254aa
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 195b4ab487c939eb32a55d9f78bc1befd100caae
workflow graph Apply filters to VCF file

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8
workflow graph Tumor-Only Detect Variants workflow

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

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 0b6e8fd8ead7644cf5398395b76af5cf4011686f
workflow graph Replace legacy AML Trio Assay

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: 233f026ffce240071edda526391be0c03186fce8