fix sigprofiler output dir + versions.yml

caravagnalab · Jan 23, 2025 · 8c96e7e · 8c96e7e
1 parent 35e03a8
commit 8c96e7e
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/conf/modules/sigprofiler.config b/conf/modules/sigprofiler.config
@@ -62,8 +62,8 @@ process {
         publishDir = [
             [
                 mode: params.publish_dir_mode,
-                path: { "${params.outdir}/signature_deconvolution/SigProfiler/${meta.id}/" }
-                //pattern: "*{txt, pdf}"
+                path: { "${params.outdir}/signature_deconvolution/SigProfiler/${meta.id}/" },
+                pattern: "results/*"
             ]
         ]
     }

diff --git a/modules/local/SigProfiler/SigProfiler/main.nf b/modules/local/SigProfiler/SigProfiler/main.nf
@@ -150,9 +150,9 @@ process SIGPROFILER {
                                 export_probabilities = bool(eval("$export_probabilities")))
 
         # save the output results
-        dest_dir = "$prefix/"
-        source_dir = "results/"
-        shutil.copytree(source_dir, dest_dir, dirs_exist_ok=True)
+        source_dir = "$prefix/"
+        dest_dir = "results/"
+        shutil.copytree(source_dir, "results", dirs_exist_ok=True)
 
         # Write version
 
@@ -161,8 +161,8 @@ process SIGPROFILER {
 
         with open('versions.yml', 'a') as f:
             f.write('"${task.process}":'+"\\n")
-            f.write("\tSigProfilerMatrixGenerator: {SigProfilerMatrixGenerator_version}\\n")
-            f.write("\tSigProfilerExtractor: {SigProfilerExtractor_version}\\n")
+            f.write("\tSigProfilerMatrixGenerator: "+SigProfilerMatrixGenerator_version+"\\n")
+            f.write("\tSigProfilerExtractor: "+SigProfilerExtractor_version+"\\n")
 
     """