doit00-init.bash

#! /bin/bash

. $(dirname ${BASH_SOURCE[0]})/doit-preamble.bash

# ------------------------------------------------------------------------
# Set up
# ------------------------------------------------------------------------

# if [ -d ${DATA} ] ; then
#     echo 1>&2 "Removing ${DATA}. Hope that's what you wanted"
#     rm -rf ${DATA}
# fi

echo 1>&2 "# Initializing ${DATA}/..."
rm -rf ${DATA}/tmp ${INPUTS}
mkdir -p ${DATA}/tmp
mkdir -p ${INPUTS}

echo 1>&2 '# Making copies of raw reads...'

cat ${NANOPORE_FQ_GZ} > ${INPUTS}/raw_nanopore.fastq.gz
if [ "${R1_FQ_GZ}" ] ; then
    cat ${R1_FQ_GZ} > ${INPUTS}/raw_short_R1.fastq.gz
fi
if [ "${R2_FQ_GZ}" ] ; then
    cat ${R2_FQ_GZ} > ${INPUTS}/raw_short_R2.fastq.gz
fi

# ------------------------------------------------------------------------
# Done.
# ------------------------------------------------------------------------

echo 1>&2 ''
echo 1>&2 '# Done.'