streamline the code with the config

moka-guys · Jan 21, 2025 · 34d5334 · 34d5334
1 parent 81003fc
commit 34d5334
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Showing 2 changed files with 15 additions and 8 deletions.
diff --git a/config/ad_config.py b/config/ad_config.py
@@ -75,6 +75,7 @@
     "email_user": os.path.join(DOCUMENT_ROOT, ".amazon_email_username"),
     "email_pw": os.path.join(DOCUMENT_ROOT, ".amazon_email_pw"),
     "dnanexus_authtoken": os.path.join(DOCUMENT_ROOT, ".dnanexus_auth_token"),
+    "adx_authtoken": ".archer_authentication_mokaguys.txt"
 }
 NOVASEQ_ID = "A01229"  # Novaseq sequencer ID
 RUNFOLDER_PATTERN = "^[0-9]{6}.*$"  # Runfolders start with 6 digits
@@ -90,6 +91,9 @@
 GATK_DOCKER = (
     "broadinstitute/gatk:4.1.8.1"  # TODO this image should have a hash added in future
 )
+ARCHER_DOCKER = (
+    "seglh/archer_api_upload:v1.0.0"
+)
 
 LANE_METRICS_SUFFIX = ".illumina_lane_metrics"
 DEMUX_NOT_REQUIRED_MSG = "%s run. Does not need demultiplexing locally"
@@ -383,6 +387,14 @@ class DemultiplexConfig(PanelConfig):
         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"
     )
+    ADX_CMD = (
+        f"docker run \
+            -v {RUNFOLDERS}/${{run_folder_name}}/Data/Intensities/BaseCalls:/data \
+            -v {DOCUMENT_ROOT}:/auth_file \
+            {ARCHER_DOCKER}  /data \
+            auth_file/{CREDENTIALS["adx_authtoken"]} \
+            ${{job_name}} 2 | tee -a {AD_LOGDIR}/archer_api_upload_logfiles/${{run_folder_name}}_archer_api_logfile.txt"
+    )
     DEMULTIPLEX_TEST_RUNFOLDERS = [
         "999999_NB552085_0496_DEMUXINTEG",
         "999999_M02353_0496_000000000-DEMUX",

diff --git a/setoff_workflows/setoff_workflows.py b/setoff_workflows/setoff_workflows.py
@@ -39,6 +39,7 @@
 from config.ad_config import SWConfig
 import logging
 from upload_runfolder.upload_runfolder import UploadRunfolder
+from config.ad_config import DemultiplexConfig
 from toolbox.toolbox import (
     return_scriptlog_config,
     test_upload_software,
@@ -912,14 +913,8 @@ def __init__(self, rf_obj: object, rf_samples: object, logger: logging.Logger):
             )  # Get SQL queries
         # Return the decision support command 
         ADX_runfolder = f"run_folder_name={self.rf_obj.runfolder_name}"
-        ADX_jobID = "job_name=$(cat /media/data3/share/${run_folder_name}/RunParameters.xml | grep -oP '(?<=ExperimentName>).*?(?=</ExperimentName)')"
-        docker = "docker run \
-                    -v /media/data3/share/${run_folder_name}/Data/Intensities/BaseCalls:/data \
-                    -v /usr/local/src/mokaguys:/auth_file \
-                    seglh/archer_api_upload:v1.0.0  /data \
-                    auth_file/.archer_authentication_mokaguys.txt \
-                    ${job_name} 2 | tee -a /usr/local/src/mokaguys/automate_demultiplexing_logfiles/archer_api_upload_logfiles/${run_folder_name}_archer_api_logfile.txt"
-
+        ADX_jobID = f"job_name=$(cat {self.rf_obj.runfolderpath}/RunParameters.xml | grep -oP '(?<=ExperimentName>).*?(?=</ExperimentName)')"
+        docker = DemultiplexConfig.ADX_CMD
         docker_api_cmd = [ADX_runfolder, ADX_jobID, docker]
         for api_cmd in docker_api_cmd:
             self.decision_support_upload_cmds.append(api_cmd)