ARGS_
to the name, and we will capitalize the name. For instance, if you named your argument your_argument_1
, you can access this in the script as $ARGS_YOUR_ARGUMENT_1
.boolean
, number
, integer
, regex
, string
.nextflow_schema.json
file, which must be stored in the root directory of your GitHub repository, to define the parameters that will be used by the workflow. These arguments will be visible on the workflow edit/details page, where you can additionally set whether the argument is required or not.
To access the argument in your script, we will prepend ARGS_
to the name, and we will capitalize the name. For instance, if you named your argument your_argument_1
, you can access this in the script as $ARGS_YOUR_ARGUMENT_1
.
For Nextflow workflows, your argument values will be written to a file named input_params.json
, which you will pass to your nextflow run
command, such as:
my_workflow_arguments.json
:$ONE_CODEX_API_KEY
is your API key,workflow_UUID
is the unique identifier for the workflow that you want to run on the sample