Modular Workflow Execution
The Tractor Nextflow Workflow is built to run the following three core modules:
- Phasing (using SHAPEIT5)
- Local Ancestry Inference (LAI) (either of RFMix2, GNomix, or FLARE)
- Tractor GWAS
- Pre-Tractor step (ancestry-specific tract extraction)
- Tractor GWAS
You can run the entire pipeline end-to-end (complete mode) run only specific modules (or combinations of them) by setting the --mode argument.
This flexibility allows you to start from different points in the workflow depending on what data you already have.
For a full example of a complete run, see: Launching an NXF Workflow.
Workflow Modes
There are 9 modes you can choose from. Each mode runs a different combination of modules and may require additional arguments depending on what data you are providing.
Remember: --lai_tool {rfmix2, gnomix, flare} is required for all modes (except phasing_only or tractor_only modes).
- Modes, Descriptions, and Required Arguments
- Additional Required Arguments Formatting
- Output Directories
Modes, Descriptions, and Required Arguments
| Mode | What it Runs | Additional Required Arguments |
|---|---|---|
complete | Full workflow: Phasing → LAI → Pre-Tractor → Tractor | As described here |
phasing_only | Phasing only (using SHAPEIT5) | No additional required arguments. |
phasing_lai | Phasing + LAI | --chr, --lai_tool |
phasing_lai_pretractor | Phasing + LAI + Pre-Tractor | --chr, --lai_tool |
lai_only | LAI only (requires phased VCF as input) | --chr, --phased_vcf, --lai_tool |
lai_pretractor | LAI + Pre-Tractor (requires phased VCF) | --chr, --phased_vcf, --lai_tool |
lai_pretractor_tractor | LAI + Pre-Tractor + Tractor (requires phased VCF) | --chr, --phased_vcf, --lai_tool |
pretractor_tractor (RFMix2/GNomix) | Pre-Tractor + Tractor using existing LAI results (phased VCF + MSP file) | --chr, --phased_vcf, --msp |
pretractor_tractor (FLARE) | Pre-Tractor + Tractor using existing FLARE results (FLARE output VCF) | --flare_anc_vcf |
tractor_only | Tractor GWAS only (requires hapcount/dosage files) | --chr, --hapdos |
Additional Required Arguments Formatting
| Argument | Description | Example |
|---|---|---|
--chr | Chromosome (chr1 or 1). Must match the naming convention used in your VCF, reference VCF, genetic map files. | --chr 22 |
--lai_tool | LAI tool to use. Options: rfmix2, gnomix, or flare. | --lai_tool rfmix2 |
--phased_vcf | Phased VCF file (with index in same directory). Index not required in pretractor_tractor mode. | --phased_vcf /path/to/phased_chr22.vcf.gz |
--msp | MSP file corresponding to the phased VCF. If --gnomix_phase=true, use the newly generated VCF. | --msp /path/to/results_chr22.msp.tsv |
--flare_anc_vcf | Phased VCF file with ancestry estimates. Input file be generated by FLARE. | --flare_anc_vcf /path/to/flare_ancestry_chr22.vcf.gz |
--hapdos | Prefix of hapdos files. The workflow detects all files automatically. Files usually follow <prefix>_<chr>.anc0.hapcount.txt. Do not include chromosome in the prefix. | If file = /path/to/results/results1_22.anc0.hapcount.txt, use: --hapdos /path/to/results/results1 |
Output Directories
All relevant output directories will be generated based on the mode used. Please see Output overview for description of all files generated.