config_run_newbler.raw_input.config 2.34 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
[interface]
classification = ng6

[parameters]
;; The run name.
$;RUN_NAME$;=
;; The run date in dd/mm/yyyy format.
$;DATE$;=
;; The species used for this run.
$;SPECIES$;=
;; The nature of the data.
$;DATA_NATURE$;=
;; The type of run done.
$;RUN_TYPE$;=
;; Run description.
$;RUN_DESCRIPTION$;=
;; The sequencer name used.
$;SEQUENCER$;=454 GS FLX XL+
;; The mids descriptions (MID1:desc1;MID2:desc2;... can also be MID1,MID2:desc;...). Leave it blank if it's not a multiplexed run.
$;MIDS_DESCRIPTIONS$; =
;; The max number of error allowed when demultiplexing
$;DEMULTIPLEXING_ERROR$; = 0
;; The project name the run belongs to. If the project already exists, the description and front end group is not required.
$;PROJECT_NAME$;=TESTBACS
;; The project description the run belongs to.
$;PROJECT_DESCRIPTION$;=
27
28
;; The project administrator login
$;ADMIN_LOGIN$; =
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67

[input]
;; The raw input to use
$;RAW_INPUT$; =
;; The path to the control fasta file, if not set no control analyze will be possible.
$;INPUT_FASTA_CONTROL_FILE$;=
;; The path to the control qual file, if not set no control analyze will be possible.
$;INPUT_QUAL_CONTROL_FILE$;=

[output]
$;OUTPUT_TOKEN$;=raw_input
$;OUTPUT_DIRECTORY$;=$;REPOSITORY_ROOT$;/output_repository/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
;; The raw input to use
$;RAW_LIST$;=$;OUTPUT_DIRECTORY$;/run.raw.list
$;CONFIG_FILE$;=$;OUTPUT_DIRECTORY$;/run.cfg
$;MIDS_CONFIG_FILE$; = $;OUTPUT_DIRECTORY$;/mids.cfg
$;ALL_MIDS_CONFIG_FILE$; = $;OUTPUT_DIRECTORY$;/all_mids.cfg
$;FASTA_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.fasta.list
$;QUAL_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.qual.list

[component]
$;COMPONENT_NAME$;=config_run_newbler
$;DESCRIPTION$;=This script is part of the ng6 project,  it creates the run config file required by all ng6 scripts 
$;WORKFLOW_REPOSITORY$;=$;REPOSITORY_ROOT$;/workflow/runtime/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
$;PIPELINE_TOKEN$;=unnamed

;The version,revision,tag here is set by an interpolated CVS tag
$;VERSION$;=$Name$
$;RELEASE_TAG$;=$Name$
$;REVISION$;=$Revision: 5503 $
$;TEMPLATE_XML$;=$;DOCS_DIR$;/$;COMPONENT_NAME$;.xml

;the following keys are replaced at runtime by the invocation script
$;COMPONENT_CONFIG$;=
$;COMPONENT_XML$;=
$;PIPELINE_XML$;=
$;PIPELINEID$;=

[include]
68
$;PROJECT_CONFIG$;=