Reduce storage used by intermediate files

[anoronh4]

Currently forte is creating large intermediate files, which are demanded by nf-core's atomized modules. I've identified a few places where the bam storage can be reduced

1. STAR_FOR_STARFUSION - we do not need to produce a bam for this process to run STARFUSION and we should probably skip writing one by default. the nf-core version of star/align currently requires a bam for the output. there's an easy fix, simply allow the bam output to be optional
2. Allow all STAR_* processes to accept multiple pairs of fastqs. That way we don't have to use samtools/merge or cat/fastq to merge read data before or after, and we can even maintain distinct read groups this way. STAR is capable of doing this, but nf-core's star/align was not written with this usage case in mind.
3. Merge the STAR_FOR_ARRIBA and ARRIBA processes together and don't output the bam at the end of the process. If scratch=true or other cleanup protocol is enabled, the bam will be discarded. Currently nf-core does not have a combined process to run arriba.

I think executing all of these will allow us to eliminate up to 5 copies of unused read data per sample, which is a huge savings in terms of storage and will possibly optimize time/compute as well. It may take some time for nf-core to adopt these changes so best to go ahead with local changes for now.

[anoronh4]

part 1 and 2 have been addressed by #15 but part 3 is still unsolved.