prepare-inputs

#!/bin/bash

# create a nice input data structure for the workflow

set -e

TOOLS_DIR=$1
INPUT_FILE=$(readlink -f $2)
TARGET_DIR=$3
TEMPLATE_NAME=$4

if ! which pigz >/dev/null 2>&1; then
    echo "Required tool, pigz, is misisng from this host!" >&2
    exit 1
fi
    
#BASE_NAME=`basename $INPUT_FILE | sed -E 's/^(forward_|reverse_)//' | sed -E 's/(_[12])*(.fastq)*(.gz)*$//g'`

echo "Outputting to $TARGET_DIR"
mkdir -p $TARGET_DIR

CMD="cat $INPUT_FILE"

# is it a gzip file?
if (file $INPUT_FILE | grep gzip) >/dev/null 2>&1; then
    CMD="$CMD | pigz -d -"
fi

# split
CMD="$CMD | $TOOLS_DIR/task-files/prepare-inputs/fastq-split-pipe $TEMPLATE_NAME"

cd $TARGET_DIR
echo "Executing: $CMD"
eval "$CMD"

exit 0