improve validation script to try to fail early with meaningful messages

[borauyar]

• Check if the settings.yaml is formatted correctly.
• Check to see if the input GTF file is parseable.
• Check transcript ids in cDNA file to see if they match transcript_id field in GTF file. Put a warning that the transcript -> gene id mapping won't work for salmon results.
• Check if chromosome naming conventions agree between the GTF file and the fasta file
  UCSC vs NCBI styles

[alexg9010]

relating to chromosome naming style checking you could have a look here: https://github.com/BIMSBbioinfo/pigx_chipseq/blob/master/scripts/Check_Config.py#L213-L267

[borauyar]

These commits fixes the issues about the annotation files:
9036ace, 014571f, efdd4f2, a7fb557

  Check if the settings.yaml is formatted correctly.
  Check to see if the input GTF file is parseable.
  Check transcript ids in cDNA file to see if they match transcript_id field in GTF file. Put a warning that the transcript -> gene id mapping won't work for salmon results.
  Check if chromosome naming conventions agree between the GTF file and the fasta file
  UCSC vs NCBI styles