run

#!/bin/bash

# Source the getopts script
source ./scripts/getopts

# Source the environment variables
source ./config/env

# Source the annotation file
source ./config/ann

# Get the current timestamp
TIMESTAMP=$(date +"%Y-%m-%d_%H.%M.%S")

# Create an output directory with the current timestamp
export OUT_DIR="output/output_$TIMESTAMP"
mkdir -p "$OUT_DIR" "$OUT_DIR"/tmp "$OUT_DIR"/annotation

# Read the parameters from the params.csv file
while IFS=',' read -r var value; do
  if [ "$var" == "future.mem" ]
  then
    MEMORY="$value"
  fi

  if [ "$var" == "future.workers" ]
  then
    WORKERS="$value"
  fi
done < config/params.csv

# Set the Seurat image based on whether ATAC is true or not
if [[ "${atac:-}" == "TRUE" ]]
then
  SEURAT_IMAGE=seurat-signac
fi

# Check if the Seurat image version tag has been supplied
if [[ -z ${SEURAT_IMAGE_VER} ]]
then
  echo -e "Seurat image version tag needs to be supplied using the -v argument.\n\nFind available versions at https://gallery.ecr.aws/chobiolab/$SEURAT_IMAGE"
  exit 1
fi

echo "Using Seurat image $SEURAT_IMAGE:$SEURAT_IMAGE_VER"

# Run the Seurat image using Singularity
singularity run \
  --no-home \
  --pwd "$APP_PATH" \
  -B "$DATA_PATH":"$DATA_PATH" \
  -B "$APP_PATH":"$APP_PATH" \
  -B ./config/params.csv:/app/config/params.csv \
  -B ./config/samples.csv:/app/config/samples.csv \
  docker://public.ecr.aws/chobiolab/"$SEURAT_IMAGE":"$SEURAT_IMAGE_VER" "$APP_PATH"/main "$@"

# Set the input directory to the current output directory and run the annotation script
INPUT=$(pwd)/"$OUT_DIR"
cd annotation || return
./run -i "$INPUT"/integrated.RDS -m "$MODEL" -w "$WORKERS" -r "$MEMORY"
cd ..

# Move the annotation output to the output directory and remove the temporary directory
mv annotation/output/output_*/* "$OUT_DIR"/annotation
rm -rf annotation/output