Autocycler table

Basics

The autocycler table command generates a TSV line from the various metrics stored in YAML files during an Autocycler assembly.

When conducting many Autocycler assemblies, you can use Autocycler cluster to build a

Example command

For this example, I assume you have conducted many Autocycler assemblies, where each sample is in a directory that starts with SAM and there is an autocycler directory in each of those:

autocycler table > metrics.tsv  // create the TSV header
for sample in SAM*; do
    autocycler table -a "$sample"/autocycler >> metrics.tsv  // append a TSV row
done

You will likely need to change the SAM* glob to whatever will catch your samples.

Full usage

Usage: autocycler table [OPTIONS]

Options:
  -a, --autocycler_dir <AUTOCYCLER_DIR>  Autocycler directory (if absent, a header line will be output)
  -f, --fields <FIELDS>                  Comma-delimited list of YAML fields to include [default: abc,def]
  -h, --help                             Print help
  -V, --version                          Print version