record conda reports env, contrast, config per analysis

R-ODAF · Jan 3, 2024 · 40aab4a · 40aab4a
1 parent fd1546d
commit 40aab4a
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/scripts/file_functions.R b/scripts/file_functions.R
@@ -16,6 +16,7 @@ set_up_paths <- function(params) {
     paths$results <- file.path(paths$output, "analysis", results_location_arg)
     paths$BMD_output <- file.path(paths$results, "BMD_and_biomarker_files")
     paths$RData <- file.path(paths$results, "RData")
+    paths$record <- file.path(paths$results, "Pipeline_record")
     paths$pathway_analysis <- file.path(paths$results, "pathway_analysis")
     lapply(paths, function(x) if(!dir.exists(x)) dir.create(x, recursive = TRUE))
     return(paths)

diff --git a/scripts/render_DESeq2_report.parallel.R b/scripts/render_DESeq2_report.parallel.R
@@ -273,5 +273,5 @@ if (!is.na(params$group_facet)) {
 system("rm -rf /tmp/intermediates_*")
 
 # save config and contrasts file too
-file.copy(file.path(paths$inputs, "config", "config.yaml"), paths$RData)
-file.copy(file.path(paths$contrasts,"contrasts.txt"), paths$RData)
+file.copy(file.path(paths$inputs, "config", "config.yaml"), paths$record)
+file.copy(file.path(paths$contrasts,"contrasts.txt"), paths$record)
diff --git a/workflow/modules/6-diffexp.smk b/workflow/modules/6-diffexp.smk
@@ -50,6 +50,8 @@ rule deseq_reports:
         '''
         rm DESeq2_complete
         Rscript scripts/render_DESeq2_report.parallel.R {analysis_folder}
+
+        conda env export > output/analysis/{analysis_folder}/Pipeline_record/reports_env.yml
         '''
 
 onerror: