Fixes instantation of Cohort when providing directory of the pipeline…

R/Cohort.R

@@ -196,10 +196,10 @@ Cohort <- R6Class("Cohort",
         warning("Pipeline report not found: ", report_path)
         return(NULL)
       }
-      
+
       # Read pipeline report
       report_lines <- readLines(report_path)
-      
+
       # Extract launch directory and samplesheet path
       launch_dir <- grep("launchDir:", report_lines, value = TRUE)
       samplesheet_path <- grep("input:", report_lines, value = TRUE)
@@ -208,12 +208,16 @@ Cohort <- R6Class("Cohort",
         warning("Could not find launch directory or samplesheet path in pipeline report")
         return(NULL)
       }
-      
+
       # Clean up paths
       launch_dir <- gsub(".*launchDir: ", "", launch_dir)
       samplesheet_filename <- gsub(".*input: ", "", samplesheet_path)
       samplesheet_filename <- gsub("^\\./", "", samplesheet_filename)
-      samplesheet_path <- file.path(launch_dir, gsub("^\\./", "", samplesheet_filename))
+      if(grepl("^/", samplesheet_filename)) { #TRUE if the samplesheet is already a full path
+          samplesheet_path <- samplesheet_filename
+      } else {
+          samplesheet_path <- file.path(launch_dir, gsub("^\\./", "", samplesheet_filename))
+      }
 
       if (!file.exists(samplesheet_path)) {
         warning("Samplesheet not found: ", samplesheet_path)
@@ -252,10 +256,10 @@ Cohort <- R6Class("Cohort",
         somatic_snvs = "sage/somatic/.*/.*sage.somatic.vcf.gz$",
         somatic_variant_annotations = "snpeff/somatic/.*/.*ann.bcf$",
         somatic_snv_cn = "snv_multiplicity3/.*/.*est_snv_cn_somatic.rds",
-        activities_sbs_signatures = "signatures/sigprofilerassignment/somatic/.*/sbs_results/.*/Assignment_Solution_Activities.txt",
+        activities_sbs_signatures = "signatures/sigprofilerassignment/somatic/.*/sbs_results/Assignment_Solution/Activities/sbs_Assignment_Solution_Activities.txt",
         matrix_sbs_signatures = "signatures/sigprofilerassignment/somatic/.*/SBS/sigmat_results.SBS96.all",
-        decomposed_sbs_signatures = "signatures/sigprofilerassignment/somatic/.*/sbs_results/.*/Decomposed_MutationType_Probabilities.txt",
-        activities_indel_signatures = "signatures/sigprofilerassignment/somatic/.*/indel_results/.*/Assignment_Solution_Activities.txt",
+        decomposed_sbs_signatures = "signatures/sigprofilerassignment/somatic/.*/sbs_results/Assignment_Solution/Activities/Decomposed_MutationType_Probabilities*.txt",
+        activities_indel_signatures = "signatures/sigprofilerassignment/somatic/.*/indel_results/Assignment_Solution/Activities/indel_Assignment_Solution_Activities.txt",
         matrix_indel_signatures = "signatures/sigprofilerassignment/somatic/.*/ID/sigmat_results.ID83.all",
         decomposed_indel_signatures = "signatures/sigprofilerassignment/somatic/.*/indel_results/.*/Decomposed_MutationType_Probabilities.txt",
         hrdetect = "hrdetect/.*/hrdetect_results.rds",

R/metadata.R

@@ -844,7 +844,13 @@ create_metadata <- function(
 ) {
     # Initialize metadata with all possible columns
     metadata <- initialize_metadata_columns(pair)
-
+    # change NA to NULL
+    fix_entries = c("tumor_type", "disease", "primary_site", "inferred_sex", "jabba_gg", "events", "somatic_snvs", "germline_snvs", "tumor_coverage", "estimate_library_complexity", "alignment_summary_metrics", "insert_size_metrics", "wgs_metrics", "het_pileups", "activities_indel_signatures", "deconstructsigs_sbs_signatures", "activities_sbs_signatures", "hrdetect", "onenesstwoness")
+    for (x in fix_entries) {
+        if (!exists(x) || is.null(get(x)) || is.na(get(x))) {
+            assign(x, NULL)
+        }
+    }    
     # Add each component sequentially
     metadata <- add_basic_metadata(metadata, tumor_type, disease, primary_site)
     metadata <- add_sex_information(metadata, inferred_sex, jabba_gg, tumor_coverage)

R/segment-width-distribution.R

@@ -18,7 +18,7 @@
 get_segstats <- function(
   balanced_jabba_gg,
   tumor_coverage,
-  coverage_field = "foreground.X",
+  coverage_field = "foreground",
   settings = internal_settings_path,
   ref = "hg19",
   max_na = 0.9,

tests/testthat/test-metadata.R

@@ -417,7 +417,8 @@ setup({
         seqnames = "chr1",
         start = 1,
         end = length(foreground_values),
-        field = "foreground.X",
+        ## field = "foreground.X",
+        field = "foreground",
         ncn = 2
     ) {
         # Create GRanges object with required structure
@@ -762,7 +763,8 @@ test_that("add_coverage_metrics processes tumor coverage correctly", {
     metadata <- initialize_metadata_columns("TEST001")
 
     # Create mock coverage data
-    mock_coverage <- list(foreground.X = c(1, 2, 1, 2, 1, 2))
+    ## mock_coverage <- list(foreground.X = c(1, 2, 1, 2, 1, 2))
+    mock_coverage <- list(foreground = c(1, 2, 1, 2, 1, 2))
     temp_file <- tempfile(fileext = ".rds")
     saveRDS(mock_coverage, temp_file)
 
@@ -836,7 +838,8 @@ test_that("add_coverage_metrics combines coverage and QC metrics", {
     metadata <- initialize_metadata_columns("TEST001")
 
     # Create mock coverage data
-    mock_coverage <- list(foreground.X = c(1, 2, 1, 2, 1, 2))
+    ## mock_coverage <- list(foreground.X = c(1, 2, 1, 2, 1, 2))
+    mock_coverage <- list(foreground = c(1, 2, 1, 2, 1, 2))
     coverage_file <- tempfile(fileext = ".rds")
     saveRDS(mock_coverage, coverage_file)
 
@@ -1539,7 +1542,7 @@ test_that("add_coverage_parameters requires purity and ploidy", {
     metadata <- initialize_metadata_columns("TEST001")
     # Note: purity and ploidy are not set
 
-    mock_coverage <- list(foreground.X = c(1, 2, 3))
+    mock_coverage <- list(foreground = c(1, 2, 3))
     temp_file <- tempfile(fileext = ".rds")
     saveRDS(mock_coverage, temp_file)