Develop

config/ad_config.py

@@ -65,10 +65,10 @@
     AD_LOGDIR = os.path.join(RUNFOLDERS, "automate_demultiplexing_logfiles")
     MAIL_SETTINGS = MAIL_SETTINGS | {  # Add test mail recipients
         "pipeline_started_subj": f"{SCRIPT_MODE}. ALERT: Started pipeline for %s",
-        "binfx_recipient": "mokaguys@gmail.com",
+        "binfx_recipient": MAIL_SETTINGS["binfx_email"],
         # Oncology email address for email alerts
-        "oncology_ops_email": "mokaguys@gmail.com",
-        "wes_samplename_emaillist": ["mokaguys@gmail.com"],
+        "oncology_ops_email": MAIL_SETTINGS["binfx_email"],
+        "wes_samplename_emaillist": MAIL_SETTINGS["binfx_email"],
     }
 
 CREDENTIALS = {
@@ -107,7 +107,7 @@
         "masked_reference": MASKED_REFERENCE,  # hs37d5_Pan4967.bwa-index.tar.gz
         "ed_vcp1_readcount_normals": f"{TOOLS_PROJECT}:file-GgKKP4Q01jZ62QgF2bbPqz78",  # Pan5208_normals_v1.0.0.RData
         "ed_vcp2_readcount_normals": f"{TOOLS_PROJECT}:file-Gbkgyq00ZpxpFKx03zVPJ9GX",  # Pan5188_normals_v1.1.0.RData
-        "ed_vcp3_readcount_normals": f"{TOOLS_PROJECT}:file-Gj62x5804G8j5Vq90q712FP9",  # Pan5217_normals_v1.0.0.RData
+        "ed_vcp3_readcount_normals": f"{TOOLS_PROJECT}:file-GvyzK780jy1Qb10KxK6kY6Gp",  # Pan5217_normals_v1.1.0.RData
         "sompy_truth_vcf": f"{TOOLS_PROJECT}:file-G7g9Pfj0jy1f87k1J1qqX83X",  # HD200_expectedsorted.vcf
     },
     "APPS": {
@@ -129,7 +129,7 @@
         "duty_csv": f"{TOOLS_PROJECT}:applet-Gp75GB00360KXPV4Jy7PPFfQ",  # duty_csv_v1.5.0
     },
     "WORKFLOWS": {
-        "pipe": f"{TOOLS_PROJECT}:workflow-GPq04280jy1k1yVkQP0fXqBg",  # GATK3.5_v2.18
+        "pipe": f"{TOOLS_PROJECT}:workflow-Gvy8YZ80jy1bb9zzb5JZBBX3",  # GATK3.5_v2.19
         "wes": f"{TOOLS_PROJECT}:workflow-FjjbQ5Q0jy1ZgyjQ3g1zgx9k",  # MokaWES_v1.8
         "snp": f"{TOOLS_PROJECT}:workflow-GB3kyJj0jy1j06704fxX9J7j",  # MokaSNP_v1.2.0
     },
@@ -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 = [
@@ -467,7 +467,7 @@ class SWConfig(PanelConfig):
     SQL_IDS = {
         # Moka IDs for generating SQLs to update the Moka database (audit trail)
         "WORKFLOWS": {
-            "pipe": 5302,
+            "pipe": 5304,
             "wes": 5078,
             "archerdx": 5300,
             "snp": 5091,

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,
         )