Create a new component

Building a reproducible Viash component.

A Viash component can be translated into one or more engines: Native, Docker; and one or more runners: Executable, Nextflow. Each of these engines and runners result in a different artifact:

Native engine: a single executable is generated which runs natively on the host system. This assumes all dependencies are already installed by the user and is therefore not reproducible. Requirements: Bash.
Docker engine: a single executable is generated but it runs inside a Docker container instead. The Docker engine specification can help you install custom dependencies and will take care of auto-mounting input/output files. Requirements: Bash, Docker.
Executable runner: a bash script is generated and can be run directly. The executable runner supports both the native and docker engine.
Nextflow runner: a Nextflow module which can be used as a standalone workflow or as a module in a larger workflow. Requirements: Nextflow and a containerization engine (e.g. Docker, Singularity, Podman).

Below we will create our first Viash component using any of the languages natively supported by Viash.

Create a script

When creating a new Viash component, you can write a new script or use a pre-existing script. Below is a script that simply copies an input file to an output destination.

Create a new file named script.sh and copy the following content inside of it. This script will copy an input file to an output destination.

#!/bin/bash

## VIASH START
par_input=path/to/file.txt
par_output=output.txt
## VIASH END

# copy file
echo "Copying '$par_input' to '$par_output'."
cp -r "$par_input" "$par_output"

Create a new file named script.csx and copy the following content inside of it. This script will copy an input file to an output destination.

using System.IO;

// VIASH START
var par = new {
  input = "path/to/file.txt",
  output = "output.txt"
};
// VIASH END

// copy file
Console.WriteLine($"Copying '{par.input}' to '{par.output}'.");
File.Copy(par.input, par.output, true);

Create a new file named script.js and copy the following content inside of it. This script will copy an input file to an output destination.

const fs = require('fs');

// VIASH START
let par = {
  'input': 'path/to/file.txt',
  'output': 'output.txt'
};
// VIASH END

// copy file
console.log(`Copying '${par['input']}' to '${par['output']}'`)
fs.copyFile(par['input'], par['output'], (err) => {
  if (err) throw err;
});

Create a new file named script.py and copy the following content inside of it. This script will copy an input file to an output destination.

import shutil

## VIASH START
par = {
  'input': 'file.txt',
  'output': 'output.txt'
}
## VIASH END

# copy file
print(f"Copying '{par['input']}' to '{par['output']}'.")
shutil.copyfile(par['input'], par['output'])

Create a new file named script.R and copy the following content inside of it. This script will copy an input file to an output destination.

## VIASH START
par <- list(
  "input" = 'file.txt',
  "output" = 'output.txt'
)
## VIASH END

# copy file
cat("Copying '", par$input, "' to '", par$output, "'.\n", sep = "")
file.copy(par$input, par$output)

Create a new file named script.scala and copy the following content inside of it. This script will copy an input file to an output destination.

import java.nio.file.StandardCopyOption.REPLACE_EXISTING
import java.nio.file.Files
import java.nio.file.Paths

// VIASH START
case class ViashPar(input: String, output: String)
val par = ViashPar(
  "path/to/file.txt",
  "output.txt"
)
// VIASH END

// copy file
println(s"Copying '${par.input}' to '${par.output}'.")
val fileIn = Paths.get(par.input)
val fileOut = Paths.get(par.output)
Files.copy(fileIn, fileOut, REPLACE_EXISTING)

Note

The par variable(s) appear to be hard coded, but they’re not! When running this script with Viash, Viash will strip away the section between VIASH START and VIASH END, and replace it with parameter values at runtime. The values included in this script are thus entirely for development and debugging purposes. More information on how this works will be given in Variables and meta-variables.

Create a config

A Viash config file is a YAML file that describes the functionality of a component as well as the engine(s) and runner(s) it targets.