enqueue_pipeline.sh 742 Bytes
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#!/bin/bash

# Enqueues COVID-19 pipelines

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CASES_FILE="data/Anonymised Combined Line List 20201117.csv"
DATE_LOW="2020-08-21"
DATE_HIGH="2020-11-13"
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TEMPLATE_CONFIG=template_config.yaml


# Job submisison
switch-gpu

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for PILLAR in both 1
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do
    for CASE_DATE_TYPE in specimen report
    do	
	RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}
	JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}"	
	qsub -N $JOB_NAME covid_pipeline.sge \
	     --reported-cases "$CASES_FILE" \
	     --case-date-type $CASE_DATE_TYPE \
	     --pillar $PILLAR \
	     --inference-period $DATE_LOW $DATE_HIGH \
	     --results-dir "$RESULTS_DIR" \
	     --output "$RESULTS_DIR/config.yaml" \
	     $TEMPLATE_CONFIG
    done
done