Explore Workflows

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

Graph Name Retrieved From View
workflow graph cnv_manta

CNV Manta calling

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

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

Branch/Commit ID: 26ae4914651d5b3e188028d1e9d88a391b3f6730
workflow graph bwa_index

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

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

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c
workflow graph FragPipe: TMT Integrator and QC

This workflow step executes TMT-Integrator using the report tables generated by Philosopher. The program applies a series of statistical filters, and high-quality thresholds to filter the data. Summary report tables are created containing peptides, proteins, genes, and phosphosites (only for phospho-enriched data sets).

 https://github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial.git

Path: FragPipe-TMT-Integrator-and-QC/fragpipe-tmt-integrator-and-qc.cwl

Branch/Commit ID: 080063b7443c98bc378935e16f747f8c542c9521
workflow graph picard_markduplicates

Mark duplicates

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

Path: structuralvariants/cwl/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c
workflow graph Run genomic CMsearch (Rfam rRNA)

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph phase VCF

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

Path: definitions/subworkflows/phase_vcf.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
workflow graph env-wf3.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: 227f35a5ed50c423afba2353871950aa61d58872
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: cd0c19d51068c5407cd70b718a561d4662819d87
workflow graph contaminant_cleanup

This workflow detect and remove contamination from a DNA fasta file

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

Path: workflows/Contamination/contaminant-cleanup.cwl

Branch/Commit ID: 11f70a71cb68b3960c2d410ba1fdcd3b8a7e1419
workflow graph createindex.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/createindex.cwl

Branch/Commit ID: 49faf55f97c8f3084b426d2db6640519d6f2ce71