specify user for docker images

config/ad_config.py

@@ -376,11 +376,11 @@ class DemultiplexConfig(PanelConfig):
     }
     TESTING = TESTING
     BCL2FASTQ2_CMD = (
-        f"docker run --rm -v %s:/mnt/run -v %s:/mnt/run/%s {BCL2FASTQ_DOCKER} -R /mnt/run "
+        f"docker run --rm --user %s:%s -v %s:/mnt/run -v %s:/mnt/run/%s {BCL2FASTQ_DOCKER} -R /mnt/run "
         "--sample-sheet /mnt/run/%s --no-lane-splitting"
     )
     CD_CMD = (
-        f"docker run --rm -v %s:/input_run {GATK_DOCKER} ./gatk CollectIlluminaLaneMetrics "
+        f"docker run --rm --user %s:%s -v %s:/input_run {GATK_DOCKER} ./gatk CollectIlluminaLaneMetrics "
         "--RUN_DIRECTORY /input_run --OUTPUT_DIRECTORY /input_run --OUTPUT_PREFIX %s"
     )
     DEMULTIPLEX_TEST_RUNFOLDERS = [

demultiplex/demultiplex.py

@@ -238,16 +238,23 @@ def __init__(self, folder_name: str, timestamp: str):
         )  # Get dictionary of loggers
         self.demux_rf_logger = self.loggers["demux"]
         self.bcl2fastq2_rf_logger = self.loggers["bcl2fastq2"]
+        #get current user to run docker images with this user instead of root
+        #controls the ownership of the files to enable deleting later
+        self.user = os.getuid()
         # N.B. --no-lane-splitting creates a single fastq for a sample,
         # not into one fastq per lane)
         self.bcl2fastq2_cmd = DemultiplexConfig.BCL2FASTQ2_CMD % (
+            self.user,
+            self.user,
             self.rf_obj.runfolderpath,
             self.rf_obj.samplesheet_path,
             self.rf_obj.samplesheet_name,
             self.rf_obj.samplesheet_name,
         )
         # Shell command to run cluster density calculation
         self.cluster_density_cmd = DemultiplexConfig.CD_CMD % (
+            self.user,
+            self.user,
             self.rf_obj.runfolderpath,
             self.rf_obj.runfolder_name,
         )