[batch]
# Batch Tag
# A tag that holds a batch file, if one has been created already
options.BATCH_TAG=clovr_lgt_batch

# Concurrent Preruns
# Number of prerun operations to run concurrently
options.CONCURRENT_PRERUN=1

# Concurrent Pipelines
# Number of pipelines to run concurrently
options.CONCURRENT_PIPELINES=10

# Concurrent Postruns
# Number of postrun steps to run concurrently
options.CONCURRENT_POSTRUN=3

# Group count
# Number of groups to split tag_list's into.  Number of files in each tag_list must be at least this large
options.GROUP_COUNT=10


[pipeline]
# Pipeline Description
# Description of pipeline
PIPELINE_DESC=Testing clovr lgt batch

# Pipeline Template
# Set that this is a batch run, do not modify
PIPELINE_TEMPLATE=clovr_batch_wrapper


[batch_pipeline]
params.DATA_DIRECTORY=/mnt/lgt_batch_test
params.DATA_OUTPUT_DIRECTORY=/diag/HLGTDBGAP/bwa_output
params.DECRYPT_SCRIPT=/mnt/user_data/decrypt/decrypt.bin
params.DECRYPT_PASSWORD=C@ncerlgt!

params.REMOTE_USER=driley
params.REMOTE_HOST=diagmaster.igs.umaryland.edu


# Input Tag
# Input tag of sequences to BLAST against
input.INPUT_TAG=hlgt_sra_files_clovr_diag_credential

# Reference tag 1
# Reference tag 1 (bacteria)
input.REF_TAG1=hlgt_bac1_remote,hlgt_bac2_remote,hlgt_bac3_remote

# Reference tag 2
# Reference tag 2 (host)
input.REF_TAG2=hlgt_human_remote

# # threads
# Number of threads to utilize for each BWA
input.THREAD_COUNT=4

# Tags to Download
# Comma separated list of tags that should be downloaded, leave the default
# Possible values: sam_files
output.TAGS_TO_DOWNLOAD=sam_files

# Pipeline Description
# Description of pipeline
pipeline.PIPELINE_DESC=

# The type of the pipeline we are running
pipeline.PIPELINE_TEMPLATE=clovr_lgt_bwa

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

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

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

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

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

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

# Credential
# Credential to use to make the cluster
cluster.CLUSTER_CREDENTIAL=clovr_diag_credential


# Terminate cluster
# Terminate a cluster automatically on successful pipeline
cluster.TERMINATE_ONFINISH=true