[batch.options]
CONCURRENT_PRERUN=1

[batch_pipeline.cluster]
MASTER_INSTANCE_TYPE=default
EXEC_INSTANCE_TYPE=default
CLUSTER_CREDENTIAL=clovr_diag_credential
EXEC_NODES=0
CLUSTER_NAME=local
MASTER_BID_PRICE=

[input]
INPUT_FILE_LIST=/mnt/staging/tags/hlgt_sra_files_clovr_diag_credential

[pipeline]
PIPELINE_WRAPPER_NAME=974609a0ee47f2109efb0cac295d72d6

[batch_pipeline.params]
DATA_OUTPUT_DIRECTORY=/diag/HLGTDBGAP/bwa_output
DECRYPT_PASSWORD=C@ncerlgt!
REMOTE_HOST=diagmaster.igs.umaryland.edu
DECRYPT_SCRIPT=/mnt/user_data/decrypt/decrypt.bin
REMOTE_USER=driley
DATA_DIRECTORY=/mnt/lgt_batch_test

[batch.options]
CONCURRENT_PIPELINES=10
GROUP_COUNT=10
CONCURRENT_POSTRUN=3
BATCH_TAG=clovr_lgt_batch
BATCH_FILE=/mnt/staging/tags/clovr_lgt_batch

[batch_pipeline.input]
INPUT_TAG=hlgt_sra_files_clovr_diag_credential
THREAD_COUNT=4
REF_FILE2=
REF_FILE1=
REF_TAG1=hlgt_bac1_remote,hlgt_bac2_remote,hlgt_bac3_remote
REF_TAG2=hlgt_human_remote

[batch_pipeline.pipeline]
PRERUN_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_lgt_bwa/clovr_lgt_bwa.prerun.xml
PIPELINE_NAME=
PIPELINE_DESC=
SOP_VERSION=clovr_lgt_bwa_version_0.0
POSTRUN_TEMPLATE_XML=/opt/clovr_pipelines/workflow/project_saved_templates/clovr_lgt_bwa/clovr_lgt_bwa.postrun.xml\
DOWNLOAD_TAG_ITERATOR_XML=/opt/ergatis/docs/clovrdownload_tag.iterator.xml
PRESTART_TEMPLATE_XML=/opt/ergatis/docs/noop.xml
PIPELINE_TEMPLATE=clovr_lgt_bwa

[pipeline]
PIPELINE_NAME=974609a0ee47f2109efb0cac295d72d6
PIPELINE_WRAPPER=None
PIPELINE_TEMPLATE=clovr_batch_wrapper
PIPELINE_DESC=Testingclovrlgtbatch

[batch_pipeline.output]
TAGS_TO_DOWNLOAD=sam_files
OUTPUT_DIR=/mnt/output

[batch_pipeline.cluster]
EXEC_BID_PRICE=
TERMINATE_ONFINISH=true