Clean up rule prepare_files_for_report

Similar to #107 (closed)

• replace \n with os.linesep
• concatenate string with os.path.join and not with +
• expand with snakemake wildcards whenever possible and avoid regular expressions
• convert it to script and use shell instead of run
• clean up in general (e.g. we cannot maintain something like this in the future:

log_lines[3] = "Filename\t" + sample_name+"|"+log_lines[3].split("\t")[1])