diff --git a/scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh b/scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh new file mode 100755 index 0000000..580e591 --- /dev/null +++ b/scripts/run_batch-code_remote-input_s3-output_s3-work_s3-fusion.sh @@ -0,0 +1,54 @@ +#!/bin/bash + +set -e + +script_name=$(basename "$0") +TMPOUT=s3://data-intuitive-tmp/test-nextflow-wave-fusion/output/${script_name%.sh} +OUT=output/${script_name%.sh} +RES=s3://data-intuitive-tmp/test-nextflow-wave-fusion/resources +WORK=s3://data-intuitive-tmp/test-nextflow-wave-fusion/work/${script_name%.sh} +NXF_CONFIG=/tmp/${script_name%.sh}.config + +# clear output dir +echo "Clearing output directory" +aws s3 rm $TMPOUT --recursive +[ -d "$OUT" ] && rm -r "$OUT" + +# run component +echo "Running component" + +cat > $NXF_CONFIG < $NXF_CONFIG < $NXF_CONFIG <