recipe biopet-fastqsplitter

This tool divides a fastq file into smaller fastq files, based on the number of output files specified.

Homepage:

https://github.com/biopet/fastq-splitter

License:

MIT

Recipe:

/biopet-fastqsplitter/meta.yaml

This tool divides a fastq file into smaller fastq files, based on the number of output files specified. For ecample, if one specifies 5 output files, it will split the fastq into 5 files of equal size. This can be very useful if one wants to use the chunking option in a pipeline: FastqSplitter can generate the exact number of fastq files (chunks) as needed.

FastqSplitter will read groups of reads (100 reads per group) and distribute this evenly over the output FASTQ files. FastqSplitter will iterate over all the output files while writing the read groups.

Example: A fastq file is split with a group size of 100 and three output files. read 1-100 will be assigned to output1 read 101-200 will be assigned to output2 read 201-300 will be assigned to output3 read 301-400 will be assigned to output1 read 401-500 will be assigned to output2 etc.

This will make sure the output fastq files are of equal size and there is no positional bias in each output file.

For documentation and manuals visit our github.io page: https://biopet.github.io/fastq-splitter

package biopet-fastqsplitter

versions:

0.1-4,  0.1-3,  0.1-2,  0.1-1

depends openjdk:

>=8,<9

depends python:

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install biopet-fastqsplitter

and update with::

   mamba update biopet-fastqsplitter

To create a new environment, run:

mamba create --name myenvname biopet-fastqsplitter

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/biopet-fastqsplitter:<tag>

(see `biopet-fastqsplitter/tags`_ for valid values for ``<tag>``)

Notes

biopet-fastqsplitter is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-fastqsplitter'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-fastqsplitter -Xms512m -Xmx1g'.

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