Mercurial > repos > jdv > albacore

comparison out_dir/configuration.cfg @ 2:b658298e65d8 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit 669955c21a5e770a6777269de6b1d2c375a704e3
author jdv
date Fri, 08 Sep 2017 10:14:40 -0400
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1:0a4f83207e53 2:b658298e65d8
1 [pipeline]
2 basecall_type = linear
3 log_summaries = false
4 log_all_intermodule_messages = false
5 desc_file = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned/layout_basecall_barcode_1d.jsn
6
7 [data_trimmer]
8 ev_window = 20
9 ev_threshold = 5
10 min_events = 3
11 delta = 2
12
13 [event_detector]
14 window1 = 4
15 window2 = 8
16 threshold1 = 1.5
17 threshold2 = 9.0
18 peak_height = 0.2
19 min_events = 1000
20 trim_front = 0
21
22 [basecaller]
23 model = template_r9.5_450bps_5mer.jsn
24 min_events = 100
25 max_events = 1000
26 overlap = 50
27 min_quality = -100.0
28 min_prob = 1e-5
29 simple_decoding = 1
30 model_path = /home/jeremy/.local/lib/python3.5/site-packages/albacore/data_versioned
31
32 [call_handler]
33 record_base = read
34 qscore_adjuster_intercept = -4.5
35 qscore_adjuster_slope = 3.0
36
37 [barcode_detector]
38 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
39 score_matrix = 4x4_mismatch_matrix.txt
40 start_gap1 = 40
41 end_gap1 = 40
42 open_gap1 = 40
43 extend_gap1 = 40
44 start_gap2 = 40
45 end_gap2 = 40
46 open_gap2 = 160
47 extend_gap2 = 160
48 min_score = 60.0
49 front_window_size = 150
50 rear_window_size = 150
51
52 [fastq]
53 header = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc}
54 header_with_barcoding = {read_id} runid={run_id} read={read_number} ch={channel_id} start_time={start_time_utc} barcode={barcode_id}
55 batch_file_name = fastq_runid_{run_id}_{batch_counter}.fastq
56 single_file_name = {read_id}.fastq
57