---
title: "Nextflow module"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Nextflow module}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
editor_options: 
  chunk_output_type: console
---

`funkyheatmap` is available as a standalone executable. The data formats
are very similar as the underlying R function. Instead of data frames
you should pass TSV files and instead of a named list (for the palettes)
you should pass a yaml file.

## Install

```bash
wget https://github.com/dynverse/funkyheatmap/releases/latest/download/nextflow.zip
unzip nextflow.zip -d funky_heatmap
```

In order for this to work, you need to have Docker and Bash installed (nothing else).


## View help

Run `--help` to get more information on the arguments of funky heatmap.

```bash
nextflow run funky_heatmap/main.nf --help
```

## Example

We also processed the `mtcars` dataset and stored it as a tsv file.
To generate a plot with it, use the following commands:

```bash
nextflow run funky_heatmap/main.nf \
  --data funky_heatmap/example_data.tsv \
  --output plot.pdf \
  --publish_dir . \
  -profile docker
```

## More information

See the [funkyheatmap home page](http://funkyheatmap.dynverse.org/) for more information and documentation.