> ## Documentation Index
> Fetch the complete documentation index at: https://developer.onecodex.com/llms.txt
> Use this file to discover all available pages before exploring further.

# Developing on One Codex

> These are a handful of good-to-know points about adapting your workflows to run on One Codex.

## Where will my FASTQ file for my input sample be located?

The FASTQ file corresponding to the `Sample` the workflow was run on will be injected into the working directory and gzip'ed. You can get the filename for the sample via the `OCX_SAMPLE_FILENAME` environment variable.

<Note>
  Whenever a file is uploaded to One Codex, the platform decompresses, validates, (optionally) interleaves, and recompresses the file using GZIP compression. That means you can always expect to use a valid GZIP'ed FASTA or FASTQ file as input in your workflow, with paired end reads interleaved one after another.

  If the uploaded file was compressed using a different compression scheme like BGZIP, that will not be retained and the file will be re-compressed with regular GZIP. If your workflow relies on a BGZIP-compressed input, you'll need to extract and recompress the file at the beginning of the workflow.
</Note>

## Containers are run as a non-root user

All workflows on One Codex run in one or more Docker containers. These containers are always run as a non-root user as part of our security model. That means certain tools or features of the operating system might not be available to your workflow, such as `ulimit`. If this prevents you from being able to run your workflow on One Codex, [reach out to us](mailto:support@onecodex.com) and we'll help you out!

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