doit16-stats.bash

#! /bin/bash

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

# ------------------------------------------------------------------------
# Compute stats
# ------------------------------------------------------------------------

rm -rf ${STATS}
mkdir -p ${STATS}

echo 1>&2 '# Compute stats...'

ARGS="-q -s"

if [ "$R2_FQ_GZ" ] ; then

    ${PIPELINE}/scripts/compute-assembly-stats \
	-t ${THREADS} \
	${ARGS} -S ${STRAIN}${VERSION} \
	${INPUTS}/raw_nanopore.fastq.gz \
	${FILTLONG}/filtered_nanopore.fastq.gz \
	${INPUTS}/raw_short_R1.fastq.gz \
	${INPUTS}/raw_short_R2.fastq.gz \
	${FASTP}/trimmed_R1.fastq.gz \
	${FASTP}/trimmed_R2.fastq.gz \
	${DATA}/final.fna \
	${DATA}/final.gff \
	| tee ${STATS}/stats.tsv

else

    ${PIPELINE}/scripts/compute-assembly-stats \
	-t ${THREADS} \
	${ARGS} -S ${STRAIN}${VERSION} \
	${INPUTS}/raw_nanopore.fastq.gz \
	${FILTLONG}/filtered_nanopore.fastq.gz \
	${INPUTS}/raw_short_R1.fastq.gz \
	"" \
	${FASTP}/trimmed_R1.fastq.gz \
	"" \
	${DATA}/final.fna \
	${DATA}/final.gff \
	| tee ${STATS}/stats.tsv

fi

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

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