Workflow Templates
Templates are ready-made workflows for common bioinformatics pipelines. Each one is a complete graph, nodes wired, sensible defaults set, that you load, point at your own inputs, and run.
Opening a template
- In the app: open the Templates panel from the left rail (or the command palette), pick a template, and it loads into a new tab. You can also start from a template when creating a workflow.
- From files: templates are plain workflow JSON, so you can download one, edit it by hand, and re-import it (or keep it in version control).
Built-in templates
| Template | Nodes | What it does |
|---|---|---|
| FASTQ QC | 10 | Read quality control with FastQC and MultiQC |
| RNA-Seq | 22 | Complete RNA sequencing analysis from reads to counts |
| Differential Expression (Salmon/Kallisto) | 14 | Transcript quantification with Salmon and Kallisto |
| DESeq2 Differential Expression | 20 | End-to-end differential expression with DESeq2 and visualization |
| Variant Calling (GATK) | 29 | Germline variant calling from FASTQ to filtered VCF |
| WGS Variant Calling | 29 | Whole genome variant calling with BWA and FreeBayes |
| Metagenomics | 31 | Taxonomic and functional profiling of microbial communities |
| Genome Assembly | 19 | De novo genome assembly with quality assessment |
| Phylogenetics | 9 | Multiple sequence alignment and phylogenetic tree construction |
| ChIP-Seq | 27 | Chromatin immunoprecipitation sequencing analysis |
| Single Cell (Cell Ranger) | 12 | 10x Genomics single cell RNA sequencing analysis |
| Spatial Transcriptomics | 6 | QC and clustering for precomputed 10x Visium outputs |
| Long Read (ONT) | 16 | Oxford Nanopore basecalling with staged local models, reference and BAM sidecars |
| WGBS Methylation | 15 | Whole-genome bisulfite sequencing with Bismark |
| Proteomics (Sage + Percolator) | 8 | DDA spectra database search with Sage, FDR estimation with Percolator |
| Metabolomics (LC-MS) | 6 | Multi-sample LC-MS with XCMS centWave peak picking |
| Pangenomics | 7 | Haplotype FASTA validation and pangenome graph building |
| CRISPR Editing | 17 | Guide RNA design, off-target screening, amplicon editing |
| Protein Structure Database | 9 | UniProt search, structure retrieval and database building |
| Synthetic Biology | 5 | SBOL 3 design import with COPASI time-course simulation |
| Biopython Analysis | 15 | Sequence parsing, statistics, translation and local BLAST |
| R Visualization | 11 | Publication-quality plots with R and ggplot2 |
| ROBUST Designer | 43 | mRNA design campaign: multi-target, multi-seed design loops with objective folding |
Templates are maintained alongside the engine, so the list grows with each release, the Templates panel in the app always shows what your version ships.
Making your own template
Any workflow can become a template:
- Build the workflow and set defaults for every parameter you want pre-filled.
- Export it as JSON (see Importing & Exporting Workflows).
- Share the file, or drop it in your workspace and import it whenever needed.
A template is just a workflow JSON document; there is no separate schema. See the Workflow JSON Format page for the full field reference.