Feature/v45.1.0

config/ad_config.py

@@ -45,7 +45,7 @@
         "pipeline_started_subj": f"{SCRIPT_MODE}. ALERT: Started pipeline for %s",
         "binfx_recipient": MAIL_SETTINGS["binfx_email"],
         # Oncology email address for email alerts
-        "oncology_ops_email": "synnovis.OncologyDutyScientist@nhs.net",
+        "oncology_ops_email": "synnovis.seglh-ods@nhs.net",
         "wes_samplename_emaillist": [
             "[email protected]",
             "[email protected]",
@@ -84,7 +84,7 @@
 SDK_SOURCE = f"source {DOCUMENT_ROOT}/apps/dx-toolkit/environment"  # dxtoolkit path
 
 # DNAnexus upload agent path
-UPLOAD_AGENT_EXE = f"{DOCUMENT_ROOT}/apps/dnanexus-upload-agent-1.5.17-linux/ua"
+UPLOAD_AGENT_EXE = "/usr/local/src/mokaguys/apps/dnanexus-upload-agent-1.5.33-linux/ua"
 BCL2FASTQ_DOCKER = "seglh/bcl2fastq2:v2.20.0.422_60dbb5a"
 GATK_DOCKER = "broadinstitute/gatk:4.1.8.1"  # TODO this image should have a hash added in future
 
@@ -112,7 +112,7 @@
         "congenica_upload": f"{TOOLS_PROJECT}:applet-G8QGBK80jy1zJK6g9yVP7P8V",  # congenica_upload_v1.3.2
         "congenica_sftp": f"{TOOLS_PROJECT}:applet-GFfJpj80jy1x1Bz1P1Bk3vQf",  # wes_congenica_sftp_upload_v1.0
         "qiagen_upload": f"{TOOLS_PROJECT}:applet-Gb6G4k00v09KXfq8f6BP7f23",  # qiagen_upload_v1.0.0
-        "oncodeep_upload": f"{TOOLS_PROJECT}:applet-GkkGQ880jy1vXXFZBFG7232G",  # oncodeep_upload v1.0.0
+        "oncodeep_upload": f"{TOOLS_PROJECT}:applet-GkkGQ880jy1vXXFZBFG7232G",  # oncodeep_upload_v1.0.0
         "upload_multiqc": f"{TOOLS_PROJECT}:applet-G2XY8QQ0p7kzvPZBJGFygP6f",  # upload_multiqc_v1.4.0
         "multiqc": f"{TOOLS_PROJECT}:applet-GXqBzg00jy1pXkQVkY027QqV",  # multiqc_v1.18.0
         "sompy": f"{TOOLS_PROJECT}:applet-G9yPb780jy1p660k6yBvQg07",  # sompy_v1.2
@@ -416,8 +416,8 @@ class SWConfig(PanelConfig):
     UPLOAD_ARGS = UPLOAD_ARGS
     RUNFOLDERS = RUNFOLDERS
     PROD_ORGANISATION = "org-viapath_prod"  # Prod org for billing
-    if BRANCH == "master":  # Prod branch
-        
+
+    if BRANCH == "main":  # Prod branch
         BSPS_ID = "BSPS_MD"
         DNANEXUS_USERS = {  # User access level
             # TODO remove InterpretationRequest user once per-user accounts set up
@@ -559,7 +559,7 @@ class ToolboxConfig(PanelConfig):
         "lane_metrics_suffix": LANE_METRICS_SUFFIX,
     }
     FLAG_FILES = {
-        "upload_started": "DNANexus_upload_started.txt",  # Holds upload agent output
+        "upload_started": "DNANexus_upload_started.txt",  # Denotes upload has started
         "bcl2fastqlog": "bcl2fastq2_output.log",  # Holds bcl2fastq2 logs
         "md5checksum": "md5checksum.txt",  # File holding checksum results
         "sscheck_flag": "sscheck_flagfile.txt",  # Denotes SampleSheet has been checked

demultiplex/README.md

@@ -23,6 +23,7 @@ It contains 2 classes:
    * SampleSheet is not empty
    * SampleSheet contains the minimum expected `[Data]` section headers: `Sample_ID, Sample_Name, index`
    * Sample name does not contain any illegal characters (in case this was not rectified after the early warning checks as this will cause bcl2fastq2 to fail)
+- If no disallowed samplesheet errors are detected, samplesheet check success or failure message is written to the `sscheck_flagfile.txt` file (if any subsequent run of the script is required, this file must be removed)
 - If the sequencer does not require an integrity check, it skips straight to `run_demultiplexing()`
 - If the sequencer does require an integrity check the following requirements must be met for `run_demultiplexing()` to be called:
   1. Checksum file generated by [integrity checking script

demultiplex/demultiplex.py

@@ -273,7 +273,7 @@ def setoff_workflow(self) -> Optional[bool]:
                     if rf_samples_obj.pipeline == "oncodeep":
                         self.copy_file(
                             self.rf_obj.masterfile_path,
-                            self.rf_obj.runfolder_masterfile_path
+                            self.rf_obj.runfolder_masterfile_path,
                         )
                         self.run_processed = True
                 return True

requirements.txt

@@ -11,6 +11,9 @@ cryptography==36.0.2
 decopatch==1.4.10
 dill==0.3.8
 dxpy==0.338.1
+Jinja2==3.1.4
+pygit2==1.12.2
+pytest-cases==3.6.14
 exceptiongroup==1.2.1
 flake8==6.1.0
 graphviz==0.20.3

setoff_workflows/README.md

@@ -66,7 +66,7 @@ Logging is performed using [ad_logger](../ad_logger/ad_logger.py).
 | sw (script_loggers) | Records script-level logs for the setoff workflows script | `TIMESTAMP_setoff_workflow.log` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/sw_script_logfiles/` |
 | sw (rf_loggers["sw"]) | Records runfolder-level logs for the setoff workflows script | `RUNFOLDERNAME_setoff_workflow.log` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/sw_script_logfiles/` |
 | dx_run_script | Records the dx run commands for processing the run. N.B. this is not written to by logging | `RUNFOLDERNAME_dx_run_commands.sh` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/dx_run_commands` |
-| decision_support_upload_cmds | Records the dx run commands to set off the Congenica upload apps. N.B. this is not written to by logging | `RUNFOLDERNAME_decision_support.sh` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/dx_run_commands` |
+| decision_support_upload_cmds | Records the dx run commands to set off the decision support upload apps. N.B. this is not written to by logging | `RUNFOLDERNAME_decision_support.sh` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/dx_run_commands` |
 | proj_creation_script | Records the commands for creating the DNAnexus project. N.B. this is not written to by logging | `RUNFOLDERNAME_create_nexus_project.sh` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/dx_run_commands` |
 
 ## Testing

upload_runfolder/README.md

@@ -82,7 +82,7 @@ self.upload_runfolder.upload_rest_of_runfolder(ignore)
 | Alias | Description | Filename | Location |
 | ------------------ | ------------------------------------------------------------------------------ | ----------------------------------------------------- | ---------------------------------------------------------------------------------- |
 | backup | Records the logs from the upload runfolder script | `RUNFOLDERNAME_upload_runfolder.log` | `/usr/local/src/mokaguys/automate_demultiplexing_logfiles/upload_runfolder_script_logfiles/` |
-| upload_agent | Records upload agent logs (stdout and stderr of the upload agent) | `DNANexus_upload_started.txt` | Within the runfolder |
+| upload_agent | Denotes runfolder upload has started | `DNANexus_upload_started.txt` | Within the runfolder |
 
 ## Testing