@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software 1.8.0 → 1.9.0

package/.turbo/turbo-build.log

@@ -1,6 +1,6 @@
  WARN  Issue while reading "/home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/.npmrc". Failed to replace env in config: ${NPMJS_TOKEN}
 
-> @platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software@1.8.0 build /home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software
+> @platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software@1.9.0 build /home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software
 > pl-pkg build
 
 info: Rendering entrypoint descriptors...
@@ -8,4 +8,4 @@
 info: Building software package 'main' for platform 'linux-x64'...
 info:   packing software into a package
 info:     generating cross-platform package
-info:   software package was written to '/home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software/pkg-platforma-open-milaboratories.run-diff-clonotype-abundance-deseq2-r.software-main-1.8.0.tgz'
+info:   software package was written to '/home/runner/work/differential-clonotype-abundance/differential-clonotype-abundance/software/pkg-platforma-open-milaboratories.run-diff-clonotype-abundance-deseq2-r.software-main-1.9.0.tgz'

package/CHANGELOG.md

@@ -1,5 +1,11 @@
 # @platforma-open/milaboratories.run-deseq2-r.software
 
+## 1.9.0
+
+### Minor Changes
+
+- 349f6fb: Updated block to capture correctly specs in latest MiXCR clonotyping exports.
+
 ## 1.8.0
 
 ### Minor Changes

package/dist/tengo/software/main.sw.json

@@ -1 +1 @@
-{"name":"@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software:main","binary":{"type":"R","registry":"platforma-open","package":"platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software/main/1.8.0.tgz","cmd":["Rscript","{pkg}/run_onlyDESeq2.R"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-r-differential-expression:main","type":"R","registry":"platforma-open","package":"platforma-open/milaboratories.runenv-r-differential-expression/main/1.0.7-{os}-{arch}.tgz","binDir":"bin"},"toolset":"renv","dependencies":{}}}
+{"name":"@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software:main","binary":{"type":"R","registry":"platforma-open","package":"platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software/main/1.9.0.tgz","cmd":["Rscript","{pkg}/run_onlyDESeq2.R"],"envVars":[],"runEnv":{"name":"@platforma-open/milaboratories.runenv-r-differential-expression:main","type":"R","registry":"platforma-open","package":"platforma-open/milaboratories.runenv-r-differential-expression/main/1.0.7-{os}-{arch}.tgz","binDir":"bin"},"toolset":"renv","dependencies":{}}}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software",
-  "version": "1.8.0",
+  "version": "1.9.0",
   "type": "module",
   "description": "Block Software: Run DESeq2 with R",
   "block-software": {

package/src/package.sw.json

@@ -0,0 +1 @@
+{"registry":"platforma-open","package":"platforma-open/milaboratories.run-diff-clonotype-abundance-deseq2-r.software/main/1.9.0.tgz"}

package/src/run_onlyDESeq2.R

@@ -44,6 +44,22 @@ option_list <- list(
 opt_parser <- OptionParser(option_list = option_list)
 opt <- parse_args(opt_parser)
 
+# Print passed arguments for debugging
+cat("--- Script Arguments ---\n")
+cat("Count matrix path:", opt$count_matrix, "\n")
+cat("Metadata path:", opt$metadata, "\n")
+cat("Contrast factor column:", opt$contrast_factor, "\n")
+cat("Numerator:", opt$numerator, "\n")
+cat("Denominator:", opt$denominator, "\n")
+cat("Output file:", opt$output, "\n")
+cat("Log2 Fold Change Threshold:", opt$fc_threshold, "\n")
+cat("Adjusted P-value Threshold:", opt$p_threshold, "\n")
+cat("Values column name:", opt$values_column, "\n")
+cat("IDs column name:", opt$IDs_column, "\n")
+cat("Minimum counts filter:", opt$min_counts, "\n")
+cat("Sample fraction for filter:", opt$fraction_for_filter, "\n")
+cat("------------------------\n\n")
+
 if (is.null(opt$count_matrix) || is.null(opt$metadata) || is.null(opt$contrast_factor) || is.null(opt$numerator) || is.null(opt$denominator)) {
   stop("Missing required arguments")
 }
@@ -73,7 +89,7 @@ colnames(metadata) <- make.names(colnames(metadata))
 
 # Transform long format to wide format
 count_matrix <- count_long %>%
-  pivot_wider(names_from = Sample, values_from = values_col) %>%
+  pivot_wider(names_from = Sample, values_from = all_of(values_col)) %>%
   as.data.frame()
 
 # Set Id columns as row name and remove it
@@ -88,7 +104,8 @@ min_samples <- max(floor(ncol(count_matrix) * filter_fraction), 1)
 count_matrix <- count_matrix[rowSums(count_matrix >= min_counts) >= min_samples, ]
 
 # For differentialclonotype abundance we add 1 as minimum clonotype count (after filtering)
-count_matrix <- replace(count_matrix, count_matrix == 0, 1)
+# count_matrix <- replace(count_matrix, count_matrix == 0, 1)
+count_matrix <- count_matrix + 1
 
 # Prepare DESeq2 dataset
 set.seed(42)