Ducks

FASTQ demultiplexer

Building

You have two options for building ducks: an assembly jar, or a native image. You probably want to check out the latest version before building anything.

$ git checkout v0.1.0

Assembly Jar

To make an assembly jar, you need sbt. Run:

$ sbt assembly 

This will produce a jar in target/scala-2.13 called something like ducks-0.1.0-assembly.jar. You can run the program then using:

$ java -jar target/scala-2.13/ducks-0.0.1-assembly.jar

Native Image

Building a binary requires a GraalVM installed as well as the native-image command. If you have GraalVM already set as your default JVM, you can install native-image with:

$ ${JAVA_HOME}/bin/gu install native-image

Then you can use targets in the make file to build a native image:

$ make

Building the native image takes some time and prints some rather ugly warnings, but it seems to make a working program. Currently the system tests use the native image.

Usage

Usage: ducks --conditions <path> --dmux-fastq <path> --data-fastq <path> [--output-dir <path>]

Demultiplexes FASTQ files based on conditions

Options and flags:
    --help
        Display this help text.
    --conditions <path>, -c <path>
        The conditions file
    --dmux-fastq <path>, -1 <path>
        The FASTQ file containing demultiplexing reads
    --data-fastq <path>, -2 <path>
        The FASTQ file containing data reads
    --output-dir <path>, -o <path>
        The output directory