Improvements to the design and defaults

[abhi18av]

Hey there :wave:

This Pull-request address important enhancements focusing on better usability and easier user interaction.

Main changes:

• Promote QC to main workflow
• Deprecate sra support (point to fetchngs)
• Move default_params
• Rename batch -> normal analysis
• Add the custom container build mechanism
• Standardize the deployment of Conda
• Remove necessity of user dealing with GATK-jar when using docker or conda.

[Mxrcon]

@abhi18av on my latest commits I tried to standardize the overall deployment of containers and conda environment as well. On conda step I added a step to register the GATK jar and check MTBseq installation. I think that the overall goals of this Pull request will be addressed by this, so I'm Kindly requesting for a review.

I published the image here: https://github.com/orgs/mtb-bioinformatics/packages/container/package/mtbseq-nf, It's published as a mtb-bioinformatics package instead of mtbseq-nf package image, as It may be complex to explain that this image is required to run mtbseq-nf but isn't the mtbseq-nf tool containerized.

[abhi18av]

Task linked: CU-2zaw8mw Finalize the improvements to design and defaults

[abhi18av]

Merging this PR after local testing