CODE:

- New mandatory input parameters added. Before only necessary fastq1, annotation and genome index, the other files we autodetected by the pipeline. Now also fastq2, annotated transcriptome index, transcriptome keys and set identifier. Done to avoid some problems the autodetection of these files involves.
- Modifications in the help to include bam as input (not finished yet) and the new mandatory parameters.
- Pipeline configuration modified to also display the new parameters and a different message if the input is FASTQ or BAM