Commit 2eff28f8 authored by Jerome Mariette's avatar Jerome Mariette
Browse files

modify config_run to create the config_run_newbler

change pipelines so there is no longer sfffile and mids_contamination_search to set
parent 6591c804
[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 Titanium
;; 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.
$;PROJECT_DESCRIPTION$;=
;; The project fe group name allowed for this project. If it doesn't exist it will be created.
$;PROJECT_FE_GROUP$;=
;; The project fe group description.
$;PROJECT_FE_GROUP_DESCRIPTION$;=
;; The project fe group parent name.
$;PROJECT_FE_GROUP_PARENT$;=
[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.
$;INPUT_QUAL_CONTROL_FILE$;=
;; The path to the mids description file, if no mids has been used in this run, left it unset.
$;INPUT_MIDS_DESCRIPTION_FILE$;=
[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
$;FASTA_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.fasta.list
$;QUAL_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.qual.list
[component]
$;COMPONENT_NAME$;=config_run
$;DESCRIPTION$;=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]
$;PROJECT_CONFIG$;=
[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 Titanium
;; 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.
$;PROJECT_DESCRIPTION$;=
;; The project fe group name allowed for this project. If it doesn't exist it will be created.
$;PROJECT_FE_GROUP$;=
;; The project fe group description.
$;PROJECT_FE_GROUP_DESCRIPTION$;=
;; The project fe group parent name.
$;PROJECT_FE_GROUP_PARENT$;=
[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.
$;INPUT_QUAL_CONTROL_FILE$;=
;; The path to the mids description file, if no mids has been used in this run, left it unset.
$;INPUT_MIDS_DESCRIPTION_FILE$;=
[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
$;FASTA_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.fasta.list
$;QUAL_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.qual.list
[component]
$;COMPONENT_NAME$;=config_run
$;DESCRIPTION$;=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]
$;PROJECT_CONFIG$;=
[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 Titanium
;; 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.
$;PROJECT_DESCRIPTION$;=
;; The project fe group name allowed for this project. If it doesn't exist it will be created.
$;PROJECT_FE_GROUP$;=
;; The project fe group description.
$;PROJECT_FE_GROUP_DESCRIPTION$;=
;; The project fe group parent name.
$;PROJECT_FE_GROUP_PARENT$;=
[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.
$;INPUT_QUAL_CONTROL_FILE$;=
;; The path to the mids description file, if no mids has been used in this run, left it unset.
$;INPUT_MIDS_DESCRIPTION_FILE$;=
[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
$;FASTA_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.fasta.list
$;QUAL_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.qual.list
[component]
$;COMPONENT_NAME$;=config_run
$;DESCRIPTION$;=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]
$;PROJECT_CONFIG$;=
[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 Titanium
;; 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.
$;PROJECT_DESCRIPTION$;=
;; The project fe group name allowed for this project. If it doesn't exist it will be created.
$;PROJECT_FE_GROUP$;=
;; The project fe group description.
$;PROJECT_FE_GROUP_DESCRIPTION$;=
;; The project fe group parent name.
$;PROJECT_FE_GROUP_PARENT$;=
[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.
$;INPUT_QUAL_CONTROL_FILE$;=
;; The path to the mids description file, if no mids has been used in this run, left it unset.
$;INPUT_MIDS_DESCRIPTION_FILE$;=
[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
$;FASTA_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.fasta.list
$;QUAL_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.qual.list
[component]
$;COMPONENT_NAME$;=config_run
$;DESCRIPTION$;=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]
$;PROJECT_CONFIG$;=
[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 Titanium
;; The project name the run belongs to. If the project already exists, the description and front end group is not required.
$;PROJECT_NAME$;=MISE
;; The project description the run belongs to.
$;PROJECT_DESCRIPTION$;=
;; The project fe group name allowed for this project. If it doesn't exist it will be created.
$;PROJECT_FE_GROUP$;=
;; The project fe group description.
$;PROJECT_FE_GROUP_DESCRIPTION$;=
;; The project fe group parent name.
$;PROJECT_FE_GROUP_PARENT$;=
[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.
$;INPUT_QUAL_CONTROL_FILE$;=
;; The path to the mids description file, if no mids has been used in this run, left it unset.
$;INPUT_MIDS_DESCRIPTION_FILE$;=
[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
$;FASTA_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.fasta.list
$;QUAL_CONTROL_LIST$;=$;OUTPUT_DIRECTORY$;/run_control.qual.list
[component]
$;COMPONENT_NAME$;=config_run
$;DESCRIPTION$;=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]
$;PROJECT_CONFIG$;=
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