config_run_newbler.config 2.24 KB
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[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.
$;SEQUENCER$; =
;; 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.
$;PROJECT_NAME$; = 
;; The project description the run belongs to.
$;PROJECT_DESCRIPTION$; =
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;; The project administrator login
$;ADMIN_LOGIN$; =
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[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]
$;OUTPUT_TOKEN$; = default
$;OUTPUT_DIRECTORY$; = $;REPOSITORY_ROOT$;/output_repository/$;COMPONENT_NAME$;/$;PIPELINEID$;_$;OUTPUT_TOKEN$;
;; The raw input to use
$;RAW_LIST$; = $;OUTPUT_DIRECTORY$;/raw_input.list
$;CONFIG_FILE$; = $;OUTPUT_DIRECTORY$;/run.cfg
$;MIDS_CONFIG_FILE$; = $;OUTPUT_DIRECTORY$;/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]
$;PROJECT_CONFIG$;=