guppy_client.yaml

# client_name (str):                    A name for the client, which will appear in server log entries.
# query_timeout (int):                  Milliseconds to wait for a server response before timing out. Default is 2000ms.
# server_file_load_timeout (int):       Seconds to wait for files to be loaded on the server. Default is 180s.
# pass_read_timeout (int):              Default value to use if the optional pass_read parameter wait_duration_ms is not supplied. The default value for this is zero, which if applied means pass_read will be non-blocking.
# connection_timeout (int):             Milliseconds to wait for a server connection attempt. Default is 15000ms.
# reconnect_timeout (int):              Seconds to wait for the client to reconnect to the server if the connection is broken. Default is 300s.
# max_message_size (int):               Size of blocks to be sent to the server, in samples. Default is 50000.
# max_reads_queued (int):               Maximum number of reads to queue for sending to the server. Default is 20.
# priority (ReadPriority):              Priority of the client (low, medium, or high). Default is medium.
# move_and_trace_enabled (bool):        Flag indicating whether to return trace and move data. Default is True.
# post_out (bool):                      Flag indicating whether to return full posterior state data. Default is False.
# barcode_kits (list):                  Strings naming each barcode kit to use. Default is to not do barcoding.
# lamp_kit (str):                       String naming LAMP barcode kit to use. Default is to not do LAMP barcoding.
# require_barcodes_both_ends (bool):    Flag indicating that barcodes must be at both ends. Default is False.
# detect_mid_strand_barcodes (bool):    Flag indicating that read will be marked as unclassified if barcodes appear within the strand itself. Default is False.
# detect_mid_strand_adapter (bool):     Flag indicating that read will be marked as unclassified if the adapter sequence appears within the strand itself. Default is False.
# min_score_barcode_front (float):      Minimum score for a front barcode to be classified. Default is 60.
# min_score_barcode_rear (float):       Minimum score for a rear barcode to be classified. Default is to use the front minimum.
# min_score_barcode_mid (float):        Minimum score for mid barcodes to be detected. Default is 50.
# detect_adapter (bool):                Enable detection of adapters at the front and rear of the sequence.
# detect_primer (bool):                 Enable detection of primers at the front and rear of the sequence.
# min_score_adapter (float):            Minimum score for a front or rear adapter to be classified. Default is 60.
# min_score_primer (float):             Minimum score for a front or rear primer to be classified. Default is 60.
# trim_barcodes (bool):                 Flag indicating that barcodes should be trimmed. Default is False.
# trim_adapters (bool):                 Flag indicating that adapters should be trimmed. Default is False.
# trim_primers (bool):                  Flag indicating that primers should be trimmed. Default is False.
# align_ref (str):                      Filename of index file to use for alignment (if any). Default is to not align.
# bed_file (str):                       Filename of BED file to use for alignment (if any). Default is to not align.
# align_type (str):                     Type of alignment requested. Valid values are "auto", "coarse", and "full". Default is "auto".
# min_score_lamp (float):               Minimum score for a LAMP barcode to be detected. Default is 80.
# min_score_lamp_mask (float):          Minimum score for a LAMP barcode mask to be detected. Default is 50.
# min_score_lamp_target (float):        Minimum score for a LAMP target to be detected. Default is 50.
# additional_lamp_context_bases (int):  Number of additional bases from context to include in lamp barcode comparison. Default is 2.

client_name: butter-eel-client_1
query_timeout: 2000
server_file_load_timeout: 180
pass_read_timeout: 0
connection_timeout: 1500
reconnect_timeout: 300
max_message_size: 50000
max_reads_queued: 20
priority: medium
move_and_trace_enabled: True
post_out: False
# barcode_kits:
# lamp_kit:
require_barcodes_both_ends: False
detect_mid_strand_barcodes: False
detect_mid_strand_adapter: False
min_score_barcode_front: 60
min_score_barcode_rear: 60
min_score_barcode_mid: 50
# detect_adapter:
# detect_primer:
min_score_adapter: 60
min_score_primer: 60
trim_barcodes: False
trim_adapters: False
trim_primers: False
# align_ref:
# bed_file:
# align_type: "auto"
min_score_lamp: 80
min_score_lamp_mask: 50
min_score_lamp_target: 50
additional_lamp_context_bases: 2