This is my (simplified) pipeline to map Nanopore FastQ reads to a reference genome (here hg38). Note that this is certainly not the best way to use Nanopore results. It's just a quick check how the results look.

minimap2_hg38_pipeline.sh

#!/bin/bash
START=$(date +%s.%N)
clear
# setup parameters

YSEQID=${PWD##*/}
# YSEQID="1234" # (the above command simply gets the name of the last segment of the current working directory)

NUM_THREADS=$(getconf _NPROCESSORS_ONLN)
echo "We can use ${NUM_THREADS} threads."

REF="/genomes/0/refseq/hg38/hg38.fa"

READS="fastq/${YSEQID}_nanopore.fastq.gz"
BAMFILE="${YSEQID}_minimap2_hg38.bam"

BAMFILE_SORTED="${YSEQID}_minimap2_hg38_sorted.bam"


# Pipeline commands:
minimap2 -t $NUM_THREADS $REF -ax map-ont $READS | \
samtools view -@ $NUM_THREADS -b -t $REF -o $BAMFILE -
samtools sort -@ $NUM_THREADS -T /var/tmp/sorted -o $BAMFILE_SORTED $BAMFILE
samtools index $BAMFILE_SORTED
samtools idxstats $BAMFILE_SORTED > ${BAMFILE_SORTED}.idxstats.tsv


# Delete no longer needed large file(s)
rm -f $BAMFILE # keep $BAMFILE_SORTED

# Easy tview file
echo "#!/bin/bash" > tview_${YSEQID}.sh
echo "samtools tview ${BAMFILE_SORTED} ${REF}" >> tview_${YSEQID}.sh
chmod a+x tview_${YSEQID}.sh

END=$(date +%s.%N)

DIFF=$(echo "$END - $START" | bc)
echo ${DIFF}