small report table fixes

stemcnv_check/app/setup_files.py

@@ -23,7 +23,6 @@ def setup_control_files(args):
                     comment_lines.append(line.rstrip())
                 else:
                     break
-        logging.info('writing sample table: ' + args.sample_table)
         with pd.ExcelWriter(args.sample_table) as writer:
             pd.DataFrame(comment_lines).to_excel(writer, index=False, header=False)
             read_sample_table(source_file, return_type='dataframe').to_excel(writer, index=False)

stemcnv_check/scripts/report_template.Rmd

@@ -198,7 +198,7 @@ make_CNV_plot_section <- function(call.table, plotsection = 'denovo') {
             # message(str_glue('N hotspots: {length(res$hotspots)}'))
             if (report_config$call.data.and.plots[[plotsection]]$include.hotspot.table & length(res$hotspots)>0) {
                 res$hotspots %>%
-                    hotspot_table_output(plotsection, row$CNV_type, high_impact_tb, highlight_tb, report_config, params$out_format) %>%
+                    hotspot_table_output(as.character(row$CNV_type), plotsection, high_impact_tb, highlight_tb, report_config, params$out_format) %>%
                     subchunkify(str_glue('CNV_call.{plotsection}.nr{i}.hotspots'))
                 cat('\n\n')
             }
@@ -269,8 +269,8 @@ repo_excl_filters <- ifelse(
 )
 
 cat(paste(
-    'Call designation takes into account the Check_Score thresholds for critical and optoinally reportable level.',
-    'Additionally, calls having an exclusion filter (i.e. below minimum size, or having a probe coverage gap) ',
+    'Call designation takes into account the Check_Score thresholds for critical and optionally reportable level.',
+    'Additionally, calls flagged with an exclusion filter (i.e. below minimum size, or having a probe coverage gap) ',
     'for a specific designation are assigend the next lower level (i.e. critical -> reportable or reportable -> no label).\n\n',
     'The current thresholds and exclsuion filters are:\n\n',
     ' - Critical Check_Score:', config$evaluation_settings$CNV_call_categorisation$check_score.critical, '\n\n',
@@ -421,8 +421,7 @@ reference_calls.table <- cnv_calls %>%
     dplyr::rename(chrom = seqnames, Size = width) %>%
     arrange(desc(Check_Score), desc(Size), chrom, start) %>%
     filter(
-        sample_id == !!sample_id & Call_label == 'Reference genotype' |
-            Call_label %in% report_config$call.data.and.plots$reference_gt$always_include
+        sample_id == !!sample_id & Call_label == 'Reference genotype'
     ) %>%
     filter(!str_detect(FILTER, refgt_filter_regex)) %>%
     mutate(i = row_number())