Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph msi_workflow.cwl

Workflow to run the MSI analysis on a batch of samples and merge the results back into a single data clinical file

https://github.com/mskcc/pluto-cwl.git

Path: cwl/msi_workflow.cwl

Branch/Commit ID: 45604eaeea15030c7302941c761464ce392abf74
workflow graph Cell Ranger Aggregate

Cell Ranger Aggregate =====================

https://github.com/datirium/workflows.git

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5
workflow graph Run pindel on provided region

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

Path: definitions/subworkflows/pindel_region.cwl

Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370
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: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479
workflow graph Run tRNAScan

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

Path: bacterial_trna/wf_trnascan.cwl

Branch/Commit ID: 2801ce53744a085580a8de91cd007c45146b51e8
workflow graph SV filtering workflow

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

Path: definitions/subworkflows/filter_sv_vcf.cwl

Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9