[input]
# Input Fasta Tag
# Tag for input
INPUT_FSA_TAG=inputfastas

# Reference database
# Reference database to use
REFERENCE_DB_TAG=clovr-prok-db


[params]
# Output prefix for the organism
# Organisms have a prefix on them
OUTPUT_PREFIX=asmbl

# Organism
# Genus and species of the organism.  Must be two words in the form of: Genus species, e.g. Escherichia coli
ORGANISM=


[cluster]
# Cluster Name
# Cluster name to run this on, shouldn't need to specify manually
CLUSTER_NAME=local

# Master Instance Type
# Instance type to use for the master, guaranteed values are 'default', 'small', 'medium', and 'large'
MASTER_INSTANCE_TYPE=default

# Master Bid Price
# If spot instances are desired, set bid price
MASTER_BID_PRICE=

# Exec Instance Type
# Instance type to use for the exec, guaranteed values are 'default', 'small', 'medium', and 'large'
EXEC_INSTANCE_TYPE=default

# Exec Bid Price
# If spot instances are desired, set bid price
EXEC_BID_PRICE=

# Number of exec nodes, should not need to specify manually
EXEC_NODES=0

# Credential
# Credential to use to make the cluster
CLUSTER_CREDENTIAL=local


[output]
# Output Directory
# Directory to download output to, this should be located in /mnt somewhere
OUTPUT_DIR=/mnt/output

# Tags to download
# The pipeline generates a number of output files, you can choose which of these outputs to download
# Possible values: polypeptide_fasta cds_fasta annotation_genbank annotation_sqn
TAGS_TO_DOWNLOAD=polypeptide_fasta,cds_fasta,annotation_genbank,annotation_sqn


[pipeline]
# Pipeline Name
# Name of pipeline
PIPELINE_NAME=ReplaceWithYourPipelineName

# Pipeline Description
# Description of pipeline
PIPELINE_DESC=

SOP_VERSION=clovr_microbe_annotation_version_1.0

PIPELINE_TEMPLATE=clovr_microbe_annotation

PRESTART_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_microbe_annotation/clovr_microbe_annotation.prestart.xml

PRERUN_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_microbe_annotation/clovr_microbe_annotation.prerun.xml

POSTRUN_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_microbe_annotation/clovr_microbe_annotation.postrun.xml

DOWNLOAD_TAG_ITERATOR_XML=/opt/ergatis/docs/clovrdownload_tag.iterator.xml