settings.py

"""Settings used in rsync_to_rdisc.py"""

""" General settings """
wkdir = "/diaggen/data/upload/"
temperror = "{}temp.error".format(wkdir)
log = "Rsync_Dx.log"
errorlog = "Rsync_Dx.errorlog"
bgarray = "/mnt/bgarray/"
alissa_vcf_upload = "/diaggen/software/production/alissa_vcf_upload/"

""" Server/user settings """
host_keys = ""
server = ["", ""]
user = ""


"""Mail finished transfer"""
email_smtp_host = "pim.umcutrecht.nl"
email_smtp_port = 25
email_from = ""
email_to = ["", ""]


""" Transfer folders  """
# folder_dic: value items
# input = hpc location,
# output = transfer location,
# files_required = list of one or more files to be checked (note that all files need to be present),
# continue_without_email = True/False boolean, in which True = continue without mail, and False = send error mail and stop
# upload_gatk_vcf = True/False, upload gatk vcf files, assumes vcf files in folder <run>/single_sample_vcf/
# upload_exomedepth_vcf = True/False, upload exomedepth vcf files, assumes vcf files in folder <run>/exomedepth/HC/
folder_dic = {
    "Exomes": {
        "input": "/hpc/diaggen/data/upload/Exomes/",
        "output": "{}/Illumina/Exomes/".format(bgarray),
        "files_required": ["workflow.done"],
        "continue_without_email": False,
        "upload_gatk_vcf": True,
        "upload_exomedepth_vcf": True,
    },
    "Genomes": {
        "input": "/hpc/diaggen/data/upload/Genomes/",
        "output": "{}/Illumina/Genomes/".format(bgarray),
        "files_required": ["workflow.done"],
        "continue_without_email": False,
        "upload_gatk_vcf": False,
        "upload_exomedepth_vcf": False,
    },
    "TRANSFER": {
        "input": "/hpc/diaggen/data/upload/TRANSFER/",
        "output": "{}/TRANSFER/".format(bgarray),
        "files_required": [""],
        "continue_without_email": False,
        "upload_gatk_vcf": False,
        "upload_exomedepth_vcf": False,
    },
    "RAW_data": {
        "input": "/hpc/diaggen/data/upload/RAW_data/",
        "output": "{}/RAW_data/BACKUP_TEMP/".format(bgarray),
        "files_required": [""],
        "continue_without_email": False,
        "upload_gatk_vcf": False,
        "upload_exomedepth_vcf": False,
    },
    "RNAseq": {
        "input": "/hpc/diaggen/data/upload/RNAseq/",
        "output": "{}/Illumina/Research_Dx/Transcriptomes/UMCU_hg38/".format(bgarray),
        "files_required": [""],
        "continue_without_email": False,
        "upload_gatk_vcf": False,
        "upload_exomedepth_vcf": False,
    },
}