added a new script for counting reads

See merge request AnnotationPipelines/riboseq_pipeline!2

Many changes: count of oligos, identification of overrepresented sequences, trimming of bases in the beginning in case of the smarter-kit protocol.

Removed cluster_log from Snakefile. Altered run_snakefile.sh. Removed unecessary generation of directories in Snakefile of process_data.

Removed cluster_log from rules in prepare_annotation Snakefile. Removed create directories rule in prepare_annotation Snakefile. Altered cluster.json in prepare_annotation Snakefile. Removed unecessary info from config.yaml in prepare_annotation Snakefile.

Addition of script that filters reads based on P-site offsets and read length and creates the A-site coverage.

Addition of script that plots the creates a read length histogram based on the mapped reads in the process data pipeline.

Addition of create_tab_delimited_CDS_file.py in the prepare annotation pipeline. Added perl script for counting riboseq reads. Needs to be further added in the process data pipeline.