Set slurm QoS based on priority of case for microSALT

    {
        "CG_ID_project": "ACC9306",
        "CG_ID_sample": "ACC9306A28",
        "Customer_ID": "cust056",
        "Customer_ID_project": 980548,
        "Customer_ID_sample": "22ET100024om",
        "application_tag": "MWRNXTR003",
        "date_arrival": "2022-01-26 00:00:00",
        "date_libprep": "2022-01-28 00:00:00",
        "date_sequencing": "2022-02-02 13:00:35",
        "method_libprep": "1764:16",
        "method_sequencing": "1830:7",
        "organism": "Neisseria spp.",
        "priority": "standard",
        "reference": "CP016017.1",
        "sequencing_qc_passed": true
    }

Config for crackeagle generated in cg with priority "stadard" as intended config.log found in crackeagle workdir:


[0|0|0] 1d [hiseq.clinical@hasta:~] [base] $ cat  /home/proj/production/microbial/results/ACC9306_2022.2.2_19.23.5/config.log 
ANALYSIS STARTED BY: B'Hiseq Clinical\N'
{
  "_comment":"Genologics temporary configuration file",
  "slurm_header":{
    "time":"12:00:00",
    "threads":"8",
    "qos":"high",
    "job_prefix":"MLST",
    "project":"production",
    "type":"core"
  },
  "regex":{
    "mail_recipient":"clinicaldelivery@scilifelab.se",
    "file_pattern":"\\w{8,12}_\\w{6,10}(?:-\\d+)*(?:\\w+)*_L\\d{1,3}_(?:R)*(\\d{1})(?:_\\d{1,3})*.fastq.gz",
    "_comment":"Organisms recognized enough to be considered stable",
    "verified_organisms":[
      "Enterococcus faecalis",
      "Enterococcus faecium",
      "Escherichia coli",
      "Klebsiella pneumoniae",
      "Staphylococcus aureus"
    ]
  },

QOS is high for entire case, seems like it is set high by default with microsalt

Seems to be populated from env file


[0|0|0] 1d [hiseq.clinical@hasta:~] [P_main] 4s $ echo $MICROSALT_CONFIG
/home/proj/production/servers/config/hasta.scilifelab.se/microSALT.json

Which seems to be the same envvar for stage and prod

[0|0|0] 1d [hiseq.clinical@hasta:~] [S_main] 3s $ echo $MICROSALT_CONFIG
/home/proj/stage/servers/config/hasta.scilifelab.se/microSALT-stage.json

Staging is low by default. Transferring this to microsalt

This part of code seems responsible https://github.com/Clinical-Genomics/microSALT/blob/2a4638f0748358e3301f064188935cf5bf7fe1d3/microSALT/utils/job_creator.py#L471

Clinical-Genomics / microSALT

Set slurm QoS based on priority of case for microSALT #154

Description

This can be closed when