Assembles a list of output file names, which will be created during reporting.
getReportFilenames(txt_folder, report_name_has_folder = TRUE)Directory where the MaxQuant output resides
Boolean: Should the report files (html, pdf) contain the name of the deepest(=last) subdirectory in 'txt_folder' which is not 'txt'? Useful for discerning different reports in a PDF viewer. E.g. when flag is FALSE: 'report_v0.91.0.html'; and 'report_v0.91.0_bloodStudy.html' when flag is TRUE (and the txt folder is '.../bloodStudy/txt/' or '...bloodStudy/', i.e. './txt/' will be skipped over)
List of output file names (just names, no file is created) with list entries: yaml_file, heatmap_values_file, R_plots_file, filename_sorting, stats_file, log_file, report_file_prefix, report_file_PDF, report_file_HTML