Explore Workflows

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

Graph Name Retrieved From View
workflow graph Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass4.cwl

Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
workflow graph Run genomic CMsearch (Rfam rRNA)

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: f10de890d1d2271299931349fa8aea660acef4ee
workflow graph alignment workflow

https://github.com/griffithlab/pmbio.org.git

Path: assets/CWL/workflow.cwl

Branch/Commit ID: 27f6d5be0a4110be1f194439163284fe08542ea6
workflow graph gathered exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle_gathered.cwl

Branch/Commit ID: e8b7759826df40b8bb821b40b15aea960a4951c4
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: e8b7759826df40b8bb821b40b15aea960a4951c4
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