Add a script to generate the index files required for pipelines

[tiagofilipe12]

Currently these index files are being generated through different instances of the pipelines, both using PlasmidUNCover and mash_wrapper.

This would ideally be made with nextflow and should handle:

• The creation of bowtie2 index and samtools index files for the fasta file with plasmids present in pATLAS.
• The generation of mash sketch for the reference fasta.
• The generation of a json file containing all the lengths of the sequences used in pATLAS.

Then, this should be provided in an URL so that docker files present in pATLASflow can be compiled and used either by pATLASflow and by assemblerflow.

Then, all the other scripts used to generate pATLAS matrix and database should also be integrated with nextflow and with this initial nextflow to generate index files required to run pATLASflow and assemblerflow processes related with pATLAS.

[tiagofilipe12]

This issue is now being addressed by this repo.