Warn user if both transcript_fasta and additional_fasta are provided.

[siddharthab]

Description of feature

Pipeline fails if a user provides --transcript_fasta "/path/to/transcript/fasta" --additional_fasta "/path/to/spike-in/fasta" --star_index false. The error will be in the salmon quantification step and will read something like:

  [2024-11-12 05:05:35.751] [jointLog] [critical] Please provide a reference FASTA file that includes all targets present in the BAM header
  If you have access to the genome FASTA and GTF used for alignment 
  consider generating a transcriptome fasta using a command like: 
  gffread -w output.fa -g genome.fa genome.gtf
  you can find the gffread utility at (http://ccb.jhu.edu/software/stringtie/gff.shtml)

This is because it is not obvious that transcript_fasta needs to be manually regenerated by the user for the spike-in, or left empty to be auto-generated.