Explore Workflows

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Graph Name Retrieved From View
workflow graph readme-genePrediction-workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_create_readme/readme-genePrediction-workflow.cwl

Branch/Commit ID: 45bb8fc5cc5e5fee3f29099469621a53d084757d
workflow graph gatk4W-copy-new.cwl

Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using GATK4. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence.

https://github.com/ambarishK/bio-cwl-tools.git

Path: gatk4W-copy-new.cwl

Branch/Commit ID: dccb12c85526c878ce3a489f9502350d187955a5
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: 700e73aaed6db1ad538dd27b2e1709f436ad3edb
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: 700e73aaed6db1ad538dd27b2e1709f436ad3edb
workflow graph Report generation workflow

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/helper/report-wf.cwl

Branch/Commit ID: f80667171aa3d9efb35d60faa4d9cdabb50ca330
workflow graph Replace legacy AML Trio Assay

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

Path: definitions/pipelines/aml_trio_cle.cwl

Branch/Commit ID: e8b7759826df40b8bb821b40b15aea960a4951c4
workflow graph Tumor-Only Detect Variants workflow

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

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 193b8de694f262ad55c7635a603c20c124748583
workflow graph CODEX analysis pipeline using Cytokit

https://github.com/hubmapconsortium/codex-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: 2d9ddc61af332c2be63e4a519d9769813f3cc57d
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: d3e4bf55753cd92f97537c7d701187ea92d1e5f0
workflow graph Example of setting up a simulation system

CWL version of the md_list.cwl workflow for HPC.

https://github.com/douglowe/biobb_hpc_cwl_md_list.git

Path: md_list.cwl

Branch/Commit ID: 95111f381617c8e63794eca42d06f10ed2605f4f