Explore Workflows

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

Graph Name Retrieved From View
workflow graph Indices builder from GBOL RDF (TTL)

Workflow to build different indices for different tools from a genome and transcriptome. This workflow expects an (annotated) genome in GBOL ttl format. Steps: - SAPP: rdf2gtf (genome fasta) - SAPP: rdf2fasta (transcripts fasta) - STAR index (Optional for Eukaryotic origin) - bowtie2 index - kallisto index

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

Path: cwl/workflows/workflow_indexbuilder.cwl

Branch/Commit ID: master
workflow graph wf_trim_and_map_pe.cwl

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

https://github.com/yeolab/eclip.git

Path: cwl/wf_trim_and_map_pe.cwl

Branch/Commit ID: master
workflow graph lobSTR-workflow.cwl

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

Path: workflows/lobSTR/lobSTR-workflow.cwl

Branch/Commit ID: lobstr-v1
workflow graph Pipeline for evaluating differential expression of genes across datasets

https://github.com/hubmapconsortium/rna-data-products.git

Path: steps/secondary-analysis.cwl

Branch/Commit ID: main
workflow graph Detect Variants workflow

https://github.com/mnneveau/cancer-genomics-workflow.git

Path: detect_variants/detect_variants.cwl

Branch/Commit ID: master
workflow graph workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: flow_dispatch/2working_files/workflow.cwl

Branch/Commit ID: master
workflow graph exome alignment and germline variant detection

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: low-vaf
workflow graph exomeseq-gatk4-01-preprocessing.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-gatk4-01-preprocessing.cwl

Branch/Commit ID: master
workflow graph EMG pipeline v3.0 (single end version)

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: ca6ca61
workflow graph tRNA_selection.cwl

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: tools/tRNA_selection.cwl

Branch/Commit ID: f993cad