Explore Workflows

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

Graph Name Retrieved From View
workflow graph Filter single sample sv vcf from depth callers(cnvkit/cnvnator)

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

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph bacterial_orthology_cond

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

Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph Non-Coding Bacterial Genes

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

Path: bacterial_noncoding/wf_bacterial_noncoding.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph bam_filtering

BAM filtering

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/bam_filtering.cwl

Branch/Commit ID: 26ae4914651d5b3e188028d1e9d88a391b3f6730
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/alignment_exome_nonhuman.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 6fad27f92dd604eca0e341178f594a560d70953b
workflow graph Nanopore read quality filter.

Workflow for nanopore read quality control and contamination filtering. Steps: - FastQC before filtering (read quality control) - Kraken2 taxonomic read classification - Minimap2 contamination filter based on given references - FastQC after filtering (read quality control)

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

Path: cwl/workflows/workflow_nanopore_quality.cwl

Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae
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: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_nonhuman.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph Metagenomic binning from assembly

Workflow for Metagenomics from raw reads to annotated bins. Steps: - MetaBAT2 (binning) - CheckM (bin completeness and contamination) - GTDB-Tk (bin taxonomic classification) - BUSCO (bin completeness)

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

Path: cwl/workflows/workflow_metagenomics_binning.cwl

Branch/Commit ID: cd0c19d51068c5407cd70b718a561d4662819d87