Merge pull request #97 from nf-core/issue_69

Remove timestamp suffix

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#82](https://github.com/nf-core/nanostring/pull/82) - Updated to nf-core template 3.0.2
+- [#96](https://github.com/nf-core/nanostring/pull/96) - Remove timestamp suffix from nacho_norm.R and write_out_prepared_gex.R
 
 ### `Dependencies`
 

bin/nacho_norm.R

@@ -38,11 +38,9 @@ get_counts <- function(
     tidyr::pivot_wider(names_from = "RCC_FILE_NAME", values_from = "Count_Norm")
 }
 
-now=format(Sys.time(), "%Y%m%d%H%M")
-
 #Write out normalized counts
 norm_counts <- as.data.frame(get_counts(nacho_data))
-write_tsv(norm_counts, file = paste0(now, "_normalized_counts.tsv"))
+write_tsv(norm_counts, file = "normalized_counts.tsv")
 
 #Write out non-hk normalized counts too
 nacho_data_no_hk <- load_rcc(data_directory = input_rcc_path,
@@ -52,4 +50,4 @@ nacho_data_no_hk <- load_rcc(data_directory = input_rcc_path,
     housekeeping_norm = FALSE)
 
 norm_counts_without_hks <- as.data.frame(get_counts(nacho_data_no_hk))
-write_tsv(norm_counts_without_hks, file = paste0(now, "_normalized_counts_wo_HKnorm.tsv"))
+write_tsv(norm_counts_without_hks, file = "normalized_counts_wo_HKnorm.tsv")

bin/write_out_prepared_gex.R

@@ -49,12 +49,11 @@ hk_annotated <- getTransposedAnnotatedCounts(counts = counts, entity = "Housekee
 endo_annotated <- getTransposedAnnotatedCounts(counts = counts, entity = "Endogenous", metadata = meta_detail)
 
 #Write files as TSVs for multiqc input :-)
-now=format(Sys.time(), "%Y%m%d%H%M")
 
 input_name <- str_c(str_split_1(tools::file_path_sans_ext(input_counts), "_")[-1], collapse = "_")
 
-write.table(hk_annotated, file = paste0(now, "_", input_name, "_Norm_GEX_HK.tsv"), sep="\t", quote = FALSE, col.names = TRUE, row.names=FALSE)
-write.table(endo_annotated, file = paste0(now, "_", input_name, "_Norm_GEX_ENDO.tsv"), sep="\t", quote = FALSE, col.names = TRUE, row.names=FALSE)
+write.table(hk_annotated, file = paste0(input_name, "_Norm_GEX_HK.tsv"), sep="\t", quote = FALSE, col.names = TRUE, row.names=FALSE)
+write.table(endo_annotated, file = paste0(input_name, "_Norm_GEX_ENDO.tsv"), sep="\t", quote = FALSE, col.names = TRUE, row.names=FALSE)
 
 prefix <- ""
 if (grepl("wo_HKnorm",input_name)) {