Accomodate the global options for customizing MTBSeq

[abhi18av]

These were mentioned here
#8 (comment)

@Mxrcon , reading the codebase for the current PR, I'm not sure if we have made use of these features at all.

This means that for example, any user would only be able to run MTBSeq with the bundled reference fasta file since

Similarly, the absence of --basecalib takes care of the base call calibration

The calibration list is stored in the directory "var/res/MTB_Base_Calibration_List.vcf" of the package. For other reference genomes, the file needs to be specified with the --basecalib OPTION or this step will be skipped.

Basically, the actual design challenge of this workflow is not the DSL2 modules etc, but the treatment of parameters. This is where you need to use creativity and experience 😉

[abhi18av]

I'd be happy to connect and discuss the overall design for this.

[Mxrcon]

yes, sure let's discuss that

[abhi18av]

As mentioned in the #8 (comment) there's one more workflow remaining for the stubs i.e. the tbfull workflow.

For this one, you can accomodate all the options as params and then we can start discussing how to accomodate those a module level since not all the parameters apply to all modules.

[Mxrcon]

Tasks:

• Populate the pipeline with standard parameters
• Add global options to the pipeline