presynaptic_n1_to_n2_with_vvd.sh

#!/bin/bash
DIR=$(cd "$(dirname "$0")"; pwd)
pushd $DIR/..

# The temporary directory needs to have 10 GB to store large Docker images
export TMPDIR="${TMPDIR:-/opt/tmp}"
export SINGULARITY_TMPDIR="${SINGULARITY_TMPDIR:-$TMPDIR}"

PROFILE=lsf
RES_DIR="/nrs/scicompsoft/rokicki/exm/results"
MODEL="/groups/dickson/dicksonlab/lillvis/ExM/Ding-Ackerman/crops-for-training_Oct2018/DING/model_DNN/saved_unet_model_2020/unet_model_synapse2020_6/unet_model_synapse2020_6.whole.h5"
BIND_FLAGS="-B /scratch -B /nrs/scicompsoft/rokicki -B $RES_DIR -B /groups/dickson/dicksonlab/lillvis"
PROJECT_CODE="dickson"

./synapse_pipeline.nf \
        -profile ${PROFILE} \
        --lsf_opts "-P $PROJECT_CODE" \
        --runtime_opts "${BIND_FLAGS}" \
        --pipeline 'presynaptic_n1_to_n2' \
        --with_vvd \
        --vvd_output_dir "${RES_DIR}/vvd" \
        --workers 3 \
        --worker_cores 1 \
        --gb_per_core 10 \
        --wait_for_spark_timeout_seconds 3600 \
        --spark_work_dir "$PWD/local" \
        --n5_compression gzip \
        --block_size '500,500,500' \
        --volume_partition_size 500 \
        --synapse_model $MODEL \
        --presynapse ${RES_DIR}/stitching/slice-tiff-s0/ch0 \
        --n1 ${RES_DIR}/stitching/slice-tiff-s0/ch1 \
        --n2 ${RES_DIR}/stitching/slice-tiff-s0/ch2 \
        --output_dir ${RES_DIR}/presynaptic_n1_to_n2 \
        -with-tower http://nextflow.int.janelia.org/api "$@"

popd