Unable to parse arguments that lack defaults in the config file

[tpadayachee]

Viash version: 0.3.0

If the code below in included in the config file of a component named 'de' and --de__species 'Mouse' is included in a Nextflow pipeline command, the parsed value of species is null instead of 'Mouse'.

   - name: "--species"
     type: string
     description: Should be either 'Mouse' or 'Human'.
     direction: input
     required: true

Changing the config file to include a default value for species (as shown below), solves the problem:

   - name: "--species"
     type: string
     description: Should be either 'Mouse' or 'Human'.
     default: "Human"
     direction: input
     required: true

[tverbeiren]

This is tackled in

• 87539bb5d9232ed9f96622719f9f7b4d39f3b839
• e722c40083bb1ddc4df6fff6685726828347391d

and will be included in a new release.

Please note that with this commit, the following logic is followed:

If an argument is required: true, it can have

• a default: ... value: It will use this default value on the CLI unless you override it on the CLI
• no default value: In this case, one has to provide a value when starting a NextFlow pipeline. Otherwise viash will give a warning and NXF will throw an error.

If an argument is required: false, it can have

• a default: ... value: It will use this default value unless you override it from the CLI
• no default value: In this case, this argument will not be present on the CLI, but it can still be overridden from the CLI