Also sync RunParameters.json

ssjunnebo · Sep 30, 2024 · f221c98 · f221c98
1 parent c86b6bf
commit f221c98
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py
@@ -437,6 +437,7 @@ def generate_demux_command(self, run_manifest, demux_dir):
             + f" {self.run_dir}"
             + f" {demux_dir}"
             + " -p 8"
+            + " --num-unassigned 500"
             + f" -r {run_manifest}"
             + " --legacy-fastq"  # TODO: except if Smart-seq3
             + " --force-index-orientation"
@@ -788,7 +789,8 @@ def aggregate_demux_results(self, demux_results_dirs):
     def sync_metadata(self):
         files_to_copy = [self.run_stats_file,
                          os.path.join(self.run_dir, "Demultiplexing", "IndexAssignment.csv"),
-                         os.path.join(self.run_dir, "Demultiplexing", "UnassignedSequences.csv")
+                         os.path.join(self.run_dir, "Demultiplexing", "UnassignedSequences.csv"),
+                         self.run_parameters_file,
                          ]
         metadata_archive = self.CONFIG.get("element_analysis").get("metadata_location") # TODO: add to aca.yaml
         dest = os.path.join(metadata_archive, self.NGI_run_id)