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: https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/9036acee3a24edc7bd1545229c2b548a737b60d0, https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/014571fa6b7457efe3e0288596859b5f5ad894c4, https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/efdd4f29a07d327a2791138025742c1c8ad4f197, https://github.com/BIMSBbioinfo/pigx_rnaseq/commit/a7fb557517e84fb7ba34cfaf6edd537ad6db8f26

  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