Nextflow version of rMVP
| Param | Default | Notes |
|---|---|---|
| genotype | file(params.genotype) | VCF Genotype file (no missing) |
| phenotype | file(params.phenotype) | Phenotype file, sep is '\t' |
| methods | "FarmCPU" | Support GLM, MLM and FarmCPU models, multiple models are separated by commas(eg. "GLM,MLM") |
| ncpus | "auto" | Number of CPU cores used, the default is the maximum number of cores - 1 |
| threshold | "0.05" | Bonfferoni correction threshold, 0.05 means the threshold line is -log10(0.05 / number of markers) |
| impute | "TRUE" | Whether to automatically imputation, if not missing will automatically skip(WARN: only applicable when there is very little data missing) |
| outdir | "result" | Output file directory |
| plot_type | "jpg" | The format of the exported picture can be "jpg", "tiff" or "pdf" |
> make test
nextflow run GWAS.nf --genotype example/mvp.vcf --phenotype example/mvp.phe --methods GLM,MLM
N E X T F L O W ~ version 20.04.1
Launching `GWAS.nf` [extravagant_rubens] - revision: 2c541b76a6
=============================================
G W A S - N F v0.1
=============================================
genotype : /Users/hyacz/Code/GWAS-pipeline/example/mvp.vcf
phenotype : /Users/hyacz/Code/GWAS-pipeline/example/mvp.phe
methods : DataflowQueue(queue=[DataflowVariable(value=GLM), DataflowVariable(value=MLM), DataflowVariable(value=groovyx.gpars.dataflow.operator.PoisonPill@20a7953c)])
ncpus : parallel::detectCores() - 1
threshold : 0.05
outdir : result
executor > local (19)
[15/e04ed9] process > DataFormatConvert [100%] 1 of 1 ✔
[dd/3224e8] process > RunAnalysis (4) [100%] 4 of 4 ✔
[e6/ad9aaa] process > FilterSignalSNP (4) [100%] 4 of 4 ✔
[28/014783] process > PlotSnpDensity [100%] 1 of 1 ✔
[39/b3707d] process > plot_phenotype_distribution [100%] 1 of 1 ✔
[1c/6c942d] process > PlotQQ (4) [100%] 4 of 4 ✔
[54/11fd83] process > PlotManhattan (4) [100%] 4 of 4 ✔
> tree result
result
├── MVP.SNP_Density.jpg
├── Phe_Distribution.T1.jpg
├── Phe_Distribution.T2.jpg
├── QQplot.T1.GLM.jpg
├── QQplot.T1.MLM.jpg
├── QQplot.T2.GLM.jpg
├── QQplot.T2.MLM.jpg
├── Rectangular-Manhattan.T1.GLM.jpg
├── Rectangular-Manhattan.T1.MLM.jpg
├── Rectangular-Manhattan.T2.GLM.jpg
├── Rectangular-Manhattan.T2.MLM.jpg
├── T1.GLM.csv
├── T1.GLM_signals.csv
├── T1.MLM.csv
├── T1.MLM_signals.csv
├── T2.GLM.csv
├── T2.GLM_signals.csv
├── T2.MLM.csv
└── T2.MLM_signals.csv