Pipeline help
There are a number of ways of getting help with gkno. Typing the command:
  • gkno
will summarize the actions that can be taken with gkno, including different ways of getting help. These help functions are summarized on this page. Note that help on all available pipelines is also available here.
Available pipelines
To see a list of all available pipelines, type:
  • gkno -api (--all-pipelines)
The flag in parentheses is the long-form of the argument. Both -api and --all-pipelines perform the same action. Executing this command will generate a list of all the different pipelines available in gkno.
To narrow down the list, we can limit ourselves to viewing only those pipelines associated with a particular category (these categories are mirrored on the website pipeline help page). To see a list of all available categories, type:
  • gkno -cat (--categories)
Then, to see all of the pipelines associated with a particular category, type:
  • gkno -cat <category>
Note that pipelines may appear in multiple categories. It is not necessary to type the full category name; gkno will list the pipelines associated with the category closest to what was typed. For example:
  • gkno -cat vcf-pr
will result in a list of all pipelines associated with the category VCF-Processing. A warning is provided to indicate that the category being displayed is not exactly what was typed (since there is no category of that name).
gkno arguments
To see all of the gkno specific (rather than pipeline specific) arguments, use the command:
  • gkno -ga
These arguments are discussed in more detail here.
Individual pipeline help
Finally, help for individual pipelines can be sought. For example:
  • gkno bwa -h (--help)
This displays the following items:
1. A brief description of the pipeline.
2. The pipeline workflow (i.e. the ordered list of performed tasks) and the tools that are used in these tasks.
3. Available parameter sets for the pipeline (see the help on parameter sets for an explanation of these).
4. A list of all the available arguments along with the expected data type and an brief description.
5. All of the values assigned to arguments from parameter sets.