Explore Workflows

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

Graph Name Retrieved From View
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a
workflow graph bacterial_screening.cwl

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

Path: vecscreen/bacterial_screening.cwl

Branch/Commit ID: 5282690e0f634a5f83107ba878fe62cbbb347408
workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

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

Path: wf_common.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: ef7f3345b352319ec22dffba26c79df033b141f9
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_apollo2_data_processing/processing/workflow.cwl

Branch/Commit ID: aa375dcaa5ccfbb4e2aa4433d10948c641b044eb
workflow graph STAR-RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq_star_fusion.cwl

Branch/Commit ID: fbeea265295ae596d5a3ba563e766be0c4fc26e8
workflow graph Nanopore assembly workflow

Workflow for sequencing with ONT nanopore, from basecalled reads to (meta)assembly and binning Steps: - Read filtering - Kraken2 (taxonomic classification of FASTQ reads) - Flye (de novo assembly) - Medaka (assembly polishing) - metaQUAST (assembly quality reports) When Illumina reads are provided: - Assembly polishing with Pilon - Metabat2 binning - CheckM - BUSCO - GTDB-Tk

https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_nanopore_assembly.cwl

Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae
workflow graph Non-Coding Bacterial Genes

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

Path: bacterial_noncoding/wf_bacterial_noncoding.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a