Command structure

virpipe [task] —-option1 —-option2 …

To run VirPipe, a task name should be written after the main virpipe command. At the end of the command line, options should be given. There are required and optional options. Without the required options, VirPipe doesn't start its run and raises an error. Optional options can be used to change some essential variables or databases.

Options are either shared by several tasks or specific to a task. On this page, shared options will be explained. Task-specific options can be found on each task page.

Shared options

Required

• --image or -i: (String) The name of the Docker image from which a container for running will be instantiated. If you follow the installation step without modifying the image name, it will always be virpipe.
• --fastq: (File) Input fastq file.
• --fastq2: (File) Second input file. This option is only used for Illumina paired-end reads. --fastq for the first fastq file and --fastq2 for the second.
• --fasta: (File) Input fasta file.
• --prefix or -p: (String) Run name. All outputs are named with this prefix.
• --platform: (String) The platform through which the input file(s) was sequenced. This option is required for the tasks that behave differently up to the platform. (choices: nanopore, illumina)

Optional

• --outdir or -o: (String) Name of output directory. All outputs will be located under outdir. If the given path doesn't exist, it will be newly created. If this option is not given, it will be copied from the value of --prefix.
• --resume or -r: (Boolean) If a run has been imperfectly completed, you can resume it from where your run left off by giving this option with the same command line before.