Aggregate demux results if more than one

SciLifeLab · Sep 17, 2024 · 32f812c · 32f812c
1 parent 5790c1a
commit 32f812c
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Showing 2 changed files with 14 additions and 7 deletions.
diff --git a/taca/analysis/analysis_element.py b/taca/analysis/analysis_element.py
@@ -74,8 +74,11 @@ def _process(run):
         elif sequencing_done and demultiplexing_status == "finished":
             transfer_status = run.get_transfer_status()
             if transfer_status == "not started":
-                #TODO: if multiple demux dir exist, move the data dirs into Demultiplexing
-                run.aggregate_demux_results()
+                demux_results_dirs = glob.glob(
+                    os.path.join(run.run_dir, "Delmultiplexing*")
+                    )
+                if len(demux_results_dirs > 1):
+                    run.aggregate_demux_results(demux_results_dirs)
                 run.sync_metadata()
                 run.make_transfer_indicator()
                 run.status = "transferring"

diff --git a/taca/element/Element_Runs.py b/taca/element/Element_Runs.py
@@ -4,6 +4,7 @@
 import re
 import zipfile
 import subprocess
+import shutil
 from datetime import datetime
 from pathlib import Path
 from glob import glob
@@ -374,14 +375,14 @@ def generate_demux_command(self, run_manifest, demux_dir):
             + " -p 8"
             + f" -r {run_manifest}"
             + " --legacy-fastq"  # TODO: except if Smart-seq3
-            + f" --force-index-orientation; echo $? > {self.rsync_exit_file}"
+            + f" --force-index-orientation"
             )  # TODO: any other options?
         return command
 
     def start_demux(self, run_manifest, demux_dir):
         with chdir(self.run_dir):
             cmd = self.generate_demux_command(run_manifest, demux_dir)
-            # TODO handle multiple composite manifests for demux
+            # TODO: handle multiple composite manifests for demux
             try:
                 p_handle = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True, cwd=self.run_dir)
                 logger.info(
@@ -426,9 +427,12 @@ def rsync_successful(self):
         else:
             return False
 
-    def aggregate_demux_results(self):
-        # TODO: aggregate demux results. Move project data dir from each sub demux dir to Demultiplexing
-        pass
+    def aggregate_demux_results(self, demux_results_dirs):
+        for demux_dir in demux_results_dirs:
+            data_dirs = [f.path for f in os.scandir(os.path.join(demux_dir, 'Samples')) if f.is_dir()]
+        for data_dir in data_dirs:
+            if not "PhiX" in data_dir and not "Unassigned" in data_dir:
+                shutil.move(data_dir, self.demux_dir)            
 
     def sync_metadata(self):
         # TODO: copy metadata from demuxed run to ngi-nas-ns