fhirproof/config.yaml at main · numlims/fhirproof · GitHub

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# fhirproof config

# sampleid sets the idcontainer code that is used for getting sampleids from json.
sampleid: SAMPLEID

# patientid sets the idcontainer code that is used for getting patientids from json.
patientid: LIMSPSN

# idcontainers lists the required idcontainers per trial and sampletype (MASTER|ALIQUOTGROUP|DERIVED)
idcontainers:
    NUM S-SNID:
        MASTER:
            - MODUL
            - TIER
            - DZHK_VISIT_NR
            - BISAMID
    NUM RAPID_REVIVE:
        MASTER:
            - BISAMID

# pamm lists the allowed aliquot materials for each primary sample material.
pamm:
    CIT:      # primary material
            - CIT # list of aliquot materials
    EDTAWB:
            - EDTA
            - EDTABUF
            - DHZB_ZB
    URN:
            - NUM_urins
            - NUM_urinf
    NUM_bal:
            - NUM_balf
            - NUM_balc
    NUM_pbmc_hep:
            - NUM_heppl
            - NUM_PBMC_C
    NUM_pbmc_cpt:
            - NUM_heppl
            - NUM_PBMC_C
    NUM_pbmc_edta:
            - NUM_PBMC_EDTAPL
            - NUM_PBMC_C
    EDTABUF:
            - NUM_DNA
    DHZB_ZB:
            - NUM_DNA
    NUM_ZB:
            - NUM_DNA
    PAXgene:
            - NUM_RNA
    NUM_pax:
            - NUM_RNA
    NUM_rachenabstrich:
            - NUM_rachenabstrich
    NUM_nasen-rachenabstrich:
            - NUM_nasen-rachenabstrich
    LH:
            - NUM_heppl
    NUM_PATHO_DIAGNOSTIC:
            - "*" # any material. some patho samples are aliquoted into diferent materials, e.g. BAL patho, into BAL zellen and BAL ueberstand, which is selected as aliquotierungsschema
    NUM_PATHO_GENETIC:
            - "*" # any material
    NUM_PATHO_ISOLATED:
            - "*" # any material
    NUM_Stuhl_nativ:
            - STL
    NUM_STOOLSWAB:
            - NUM_STOOLSWAB
    NUM_liquor:
            - NUM_liquorf
    SER:
            - SER

alicontainers: # allowed aliquot containers
    - NUM_AliContainer
    - NUMCryoAliquot500
    - NUMCryoAliquot300
    - NUMAliquot1000
    - NUMAliquot2000