Read version info from nf-core/demultiplex version file

bin/get_metadata.py

@@ -6,6 +6,8 @@
 import argparse
 import os
 import json
+from pathlib import Path
+import yaml
 
 
 class RunfolderInfo:
@@ -82,6 +84,14 @@ def get_bcl2fastq_version(self, runfolder):
             bcl2fastq_str = f.read()
         return bcl2fastq_str.split("v")[1].strip()
 
+    def get_software_version(self, runfolder):
+        with open(Path(runfolder) / "pipeline_info" / "software_versions.yml") as f:
+            return {
+                software: version
+                for software_dict in yaml.safe_load(f).values()
+                for software, version in software_dict.items()
+            }
+
     def get_run_parameters(self):
         results = OrderedDict()
         for key, value in self.run_parameters_tags.items():
@@ -116,10 +126,26 @@ def get_info(self):
         flowcell_type = self.find_flowcell_type_novaseqx()
         if flowcell_type:
             results.update(flowcell_type)
-        if os.path.exists(os.path.join(self.runfolder, "bcl2fastq_version")):
-            results["bcl2fastq version"] = self.get_bcl2fastq_version(self.runfolder)
+
         return results
 
+    def get_demultiplexing_info(self):
+        try:
+            return {
+                "Demultiplexing": {
+                    "bcl2fastq": self.get_bcl2fastq_version(self.runfolder)
+                }
+            }
+        except FileNotFoundError:
+            pass
+
+        try:
+            return {"Demultiplexing": self.get_software_version(self.runfolder)}
+        except FileNotFoundError:
+            pass
+
+        return {}
+
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description="Dumps a metadata yaml for MultiQC")
@@ -138,7 +164,7 @@ def get_info(self):
     bcl2fastq_outdir = args.bcl2fastq_outdir
 
     runfolder_info = RunfolderInfo(runfolder, bcl2fastq_outdir)
-    results = runfolder_info.get_info()
+    info = runfolder_info.get_info()
 
     print(
         """
@@ -150,6 +176,11 @@ def get_info(self):
     <dl class="dl-horizontal">
 """
     )
-    for k, v in results.items():
-        print("        <dt>{}</dt><dd><samp>{}</samp></dd>".format(k, v))
+    for k, v in info.items():
+        print(f"        <dt>{k}</dt><dd><samp>{v}</samp></dd>")
+
+    print("        <dt>Demultiplexing</dt>")
+    for software, version in runfolder_info.get_demultiplexing_info().items():
+        print(f"            <dd>{software}: <samp>{version}</samp></dd>")
+
     print("    </dl>")

test_data/210510_M03910_0104_000000000-JHGJL/pipeline_info/software_versions.yml

@@ -0,0 +1,8 @@
+BCL2FASTQ:
+  bcl2fastq: 2.20.0.422
+CUSTOM_DUMPSOFTWAREVERSIONS:
+  python: 3.12.0
+  yaml: 6.0.1
+Workflow:
+  Nextflow: 23.04.3
+  nf-core/demultiplex: 1.5.0dev

tests/unit_tests/test_get_metadata.py

@@ -58,6 +58,20 @@ def test_bcl2fastq_version(runfolder_info):
     assert bcl2fastq_version == "2.20.0.422"
 
 
+def test_get_software_version(runfolder_info):
+    software_versions = runfolder_info.get_software_version(
+        "test_data/210510_M03910_0104_000000000-JHGJL"
+    )
+
+    assert software_versions == {
+        "bcl2fastq": "2.20.0.422",
+        "python": "3.12.0",
+        "yaml": "6.0.1",
+        "Nextflow": "23.04.3",
+        "nf-core/demultiplex": "1.5.0dev",
+    }
+
+
 def test_get_run_parameters(runfolder_info):
     filtered_run_parameters = runfolder_info.get_run_parameters()
     assert len(filtered_run_parameters) == 5
@@ -95,4 +109,4 @@ def test_get_read_cycles(runfolder_info):
 
 def test_get_info(runfolder_info):
     results = runfolder_info.get_info()
-    assert len(results) == 10
+    assert len(results) == 9