utils: ave_gene_cov bug

Fix function ave_gene_cov in utils.py: https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/master/workflow/scripts/utils.py#L284

1. why using if contig_id != ""?: https://git-r3lab.uni.lu/susheel.busi/ont_pilot_gitlab/-/blob/master/workflow/scripts/utils.py#L299
2. no ave. cov. for genes/proteins from the last contig because the if statement will not be reached after the end of file

• fix the code
• re-create the per-gene coverage result files
• compare to prev. result files
• re-run the report workflow
• re-run the figure workflow
• update notes
• add relevant per-gene cov. files to result archive (also update its README)
• re-create the result archive (update on figshare)
• re-create the code archive (update on figshare)
• update figures (if needed) in the manuscript