Explore Workflows

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

Graph Name Retrieved From View
workflow graph rnaseq-alignment-quantification

This workflow retrieve SRA fastqc data and execute QC, alignment and quantification from TPMCalculator

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/RNA-Seq/rnaseq-quantification-qc.cwl

Branch/Commit ID: 8967e816cb89dd9349c8c6deff686aeb8b118f1c
workflow graph Unaligned BAM to BQSR

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: ffd73951157c61c1581d346628d75b61cdd04141
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: 509938802c5e42bb8084c6a5a26ab6425c60e69a
workflow graph Whole genome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_wgs.cwl

Branch/Commit ID: f0cdc773e31e4aa116838e8aba4954c31bd3d68b
workflow graph strelkaSomaticVariantCaller_v0_1_1.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl

Branch/Commit ID: 1d45492ae0085824a7ac532d0dfa6621c1cbe415
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: f45b52a24c7b54a75368dcbab24b4eb2c5a9c75a
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: c625e05eefb1754353c1bdfa46c01dc61e6233dd
workflow graph tt_fscr_calls_pass1

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

Path: task_types/tt_fscr_calls_pass1.cwl

Branch/Commit ID: 7cee09fb3e33c851e4e1dfc965c558b82290a785
workflow graph Detect Variants workflow for WGS pipeline

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

Path: definitions/pipelines/detect_variants_wgs.cwl

Branch/Commit ID: c625e05eefb1754353c1bdfa46c01dc61e6233dd
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: c625e05eefb1754353c1bdfa46c01dc61e6233dd