fix sigprofiler module + mc subworkflow

caravagnalab · Jan 22, 2025 · 6307915 · 6307915
1 parent 3e5ca68
commit 6307915
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/modules/local/SigProfiler/SigProfiler/main.nf b/modules/local/SigProfiler/SigProfiler/main.nf
@@ -56,6 +56,7 @@ process SIGPROFILER {
     import shutil
     import pandas as pd
     import multiprocessing
+    from importlib.metadata import version
     from SigProfilerExtractor import sigpro as sig
     from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as matGen
 
@@ -154,12 +155,15 @@ process SIGPROFILER {
         shutil.copytree(source_dir, dest_dir, dirs_exist_ok=True)
 
         # Write version
-        SigProfilerMatrixGenerator_version = os.popen("pip show SigProfilerMatrixGenerator | grep Version | awk '{print $NF}'").read().strip()
-        SigProfilerExtractor_version = os.popen("pip show SigProfilerExtractor | grep Version | awk '{print $NF}'").read().strip()
-        with open("versions.yml", "w") as f:
-            f.write(f'"$task.process":\n')
-            f.write(f'    SigProfilerMatrixGenerator: {SigProfierMatrixGenerator_version}\n')
-            f.write(f'    SigProfilerExtractor: {SigProfilerExtractor_version}\n')
+
+        SigProfilerMatrixGenerator_version = version("SigProfilerMatrixGenerator")
+        SigProfilerExtractor_version = version("SigProfilerExtractor")
+
+        with open('versions.yml', 'a') as f:
+            f.write('"${task.process}":'+"\\n")
+            f.write("\tSigProfilerMatrixGenerator: {SigProfilerMatrixGenerator_version}\\n")
+            f.write("\tSigProfilerExtractor: {SigProfilerExtractor_version}\\n")
+
     """
 
 }
diff --git a/subworkflows/local/signature_deconvolution/main.nf b/subworkflows/local/signature_deconvolution/main.nf
@@ -54,7 +54,8 @@ workflow SIGNATURE_DECONVOLUTION {
             [meta.subMap('dataset', 'id'), tsv]}
             | groupTuple
 
-        Sigprofiler_out = SIGPROFILER(input_sigprofiler, genome_path)
+        SIGPROFILER(input_sigprofiler, genome_path)
+        Sigprofiler_out = SIGPROFILER.out.sigprofiler_results
     }
 
     emit: