doit12-unicycler.bash

#! /bin/bash

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

# ------------------------------------------------------------------------
# Run unicycler (for a second opinion on the assembly)
# ------------------------------------------------------------------------

if [ -z "${R1_FQ_GZ}" ] ; then

    echo 1>&2 '# No Illumina reads. Skipping unicycler.'

else

    echo 1>&2 '# Running unicycler'

    rm -rf ${UNICYCLER}
    mkdir ${UNICYCLER}

    unicycler -t ${THREADS} \
	      -1 ${FASTP}/trimmed_R1.fastq.gz \
	      -2 ${FASTP}/trimmed_R2.fastq.gz \
	      -l ${FILTLONG}/filtered_nanopore.fastq.gz \
	      -o ${UNICYCLER}

    if [ -e ${DATA}/assembly.fasta ] ; then
	echo 1>&2 '# Running DNADiff against Trycycler assembly'

	mkdir ${UNICYCLER}/dnadiff
	cp ${DATA}/assembly.fasta ${UNICYCLER}/dnadiff/trycycler.fasta
	cp ${UNICYCLER}/assembly.fasta ${UNICYCLER}/dnadiff/unicycler.fasta
	cd ${UNICYCLER}/dnadiff
	dnadiff trycycler.fasta unicycler.fasta
	echo ''
	cat out.report
    fi

fi

# ------------------------------------------------------------------------


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

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