Developing 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.

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A note on file compression

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.

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 and we'll help you out!