Lowercase pcs in results csv (#117)

Author: kachulis

ImputationPipeline/AggregatePRSResults.wdl

@@ -80,7 +80,7 @@ task AggregateResults {
     results <- c("~{sep='","' results}") %>% map(read_csv, col_types=cols(is_control_sample='l', .default='c')) %>% reduce(bind_rows)
     target_pcs <- c("~{sep='","' target_pc_projections}") %>% map(read_tsv) %>% reduce(bind_rows) %>% select(-FID) %>% rename(sample_id = IID)
 
-    results <- inner_join(results, target_pcs)
+    results <- inner_join(results, target_pcs) %>% rename_with(tolower, starts_with("PC"))
 
     lab_batch <- results %>% pull(lab_batch) %>% unique()
 
@@ -103,7 +103,7 @@ task AggregateResults {
 
     write_tsv(results %>% filter(is_control_sample), "~{output_prefix}_control_results.tsv")
 
-    results_pivoted <- results %>% select(-starts_with("PC")) %>% filter(!is_control_sample) %>% pivot_longer(!c(sample_id, lab_batch, is_control_sample), names_to=c("condition",".value"), names_pattern="(.+)(?<!not)(?<!reason)_(.+)$")
+    results_pivoted <- results %>% select(-starts_with("pc")) %>% filter(!is_control_sample) %>% pivot_longer(!c(sample_id, lab_batch, is_control_sample), names_to=c("condition",".value"), names_pattern="(.+)(?<!not)(?<!reason)_(.+)$")
     results_pivoted <- results_pivoted %T>% {options(warn=-1)} %>% mutate(adjusted = as.numeric(adjusted),
                                                                           raw = as.numeric(raw),
                                                                           percentile = as.numeric(percentile)) %T>% {options(warn=0)}

test/AggregatePRSResults/plumbing_data/expected_batch_all_results.tsv

@@ -1,4 +1,4 @@
-sample_id	lab_batch	is_control_sample	condition_1_raw	condition_1_adjusted	condition_1_percentile	condition_1_risk	condition_1_reason_not_resulted	condition_2_raw	condition_2_adjusted	condition_2_percentile	condition_2_risk	condition_2_reason_not_resulted	condition_3_raw	condition_3_adjusted	condition_3_percentile	condition_3_risk	condition_3_reason_not_resulted	condition_4_raw	condition_4_adjusted	condition_4_percentile	condition_4_risk	condition_4_reason_not_resulted	PC1	PC2	PC3	PC4
+sample_id	lab_batch	is_control_sample	condition_1_raw	condition_1_adjusted	condition_1_percentile	condition_1_risk	condition_1_reason_not_resulted	condition_2_raw	condition_2_adjusted	condition_2_percentile	condition_2_risk	condition_2_reason_not_resulted	condition_3_raw	condition_3_adjusted	condition_3_percentile	condition_3_risk	condition_3_reason_not_resulted	condition_4_raw	condition_4_adjusted	condition_4_percentile	condition_4_risk	condition_4_reason_not_resulted	pc1	pc2	pc3	pc4
 sample_1	test_batch	FALSE	49.8	-0.5	0.308	NOT_HIGH	NA	-0.09	-1.8	0.036	NOT_HIGH	NA	-0.3	-0.7	0.24	NOT_HIGH	NA	NA	NA	NA	NA	NA	0.13	-0.15	-0.05	-0.02
 sample_2	test_batch	TRUE	51.2	2.1	0.98	HIGH	NA	1.97	0.9	0.82	NOT_HIGH	NA	-0.2	-0.3	0.38	NOT_HIGH	NA	1.23	0.32	0.63	NOT_HIGH	NA	0.12	-0.15	-0.05	-0.03
 sample_3	test_batch	FALSE	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	NA	1.2	-0.03	0.48	NOT_HIGH	NA	0.11	-0.15	-0.05	-0.03

test/AggregatePRSResults/plumbing_data/expected_batch_control_results.tsv

@@ -1,2 +1,2 @@
-sample_id	lab_batch	is_control_sample	condition_1_raw	condition_1_adjusted	condition_1_percentile	condition_1_risk	condition_1_reason_not_resulted	condition_2_raw	condition_2_adjusted	condition_2_percentile	condition_2_risk	condition_2_reason_not_resulted	condition_3_raw	condition_3_adjusted	condition_3_percentile	condition_3_risk	condition_3_reason_not_resulted	condition_4_raw	condition_4_adjusted	condition_4_percentile	condition_4_risk	condition_4_reason_not_resulted	PC1	PC2	PC3	PC4
+sample_id	lab_batch	is_control_sample	condition_1_raw	condition_1_adjusted	condition_1_percentile	condition_1_risk	condition_1_reason_not_resulted	condition_2_raw	condition_2_adjusted	condition_2_percentile	condition_2_risk	condition_2_reason_not_resulted	condition_3_raw	condition_3_adjusted	condition_3_percentile	condition_3_risk	condition_3_reason_not_resulted	condition_4_raw	condition_4_adjusted	condition_4_percentile	condition_4_risk	condition_4_reason_not_resulted	pc1	pc2	pc3	pc4
 sample_2	test_batch	TRUE	51.2	2.1	0.98	HIGH	NA	1.97	0.9	0.82	NOT_HIGH	NA	-0.2	-0.3	0.38	NOT_HIGH	NA	1.23	0.32	0.63	NOT_HIGH	NA	0.12	-0.15	-0.05	-0.03