[pipeline]
basecall_type = linear
log_summaries = false
log_all_intermodule_messages = false
desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_basecall_barcode_1d.jsn

[data_trimmer]
ev_window = 20
ev_threshold = 5
min_events = 3
delta = 2

[event_detector]
window1 = 4
window2 = 8
threshold1 = 1.5
threshold2 = 9.0
peak_height = 0.2
min_events = 1000
trim_front = 0

[basecaller]
model = template_r9.5_450bps_5mer.jsn
min_events = 100
max_events = 1000
overlap = 50
min_quality = -100.0
min_prob = 1e-5
simple_decoding = 1
model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned

[call_handler]
record_base = read
qscore_adjuster_intercept = -4.5
qscore_adjuster_slope = 3.0

[barcode_detector]
arrangements_files = barcode_arrs_pcr96.cfg barcode_arrs_nb.cfg barcode_arrs_rbk.cfg barcode_arrs_lwb.cfg barcode_arrs_rlb.cfg barcode_arrs_rab.cfg
score_matrix = 4x4_mismatch_matrix.txt
start_gap1 = 40
end_gap1 = 40
open_gap1 = 40
extend_gap1 = 40
start_gap2 = 40
end_gap2 = 40
open_gap2 = 160
extend_gap2 = 160
min_score = 60.0
front_window_size = 150
rear_window_size = 150

[fastq]
header = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
header_with_barcoding = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
batch_file_name = fastq_runid_{run_id}_{batch_counter}.fastq
single_file_name = {read_id}.fastq