Improve performance when running slurm jobs on uppmax

[thokall]

# copy the index files used in the analysis to $SNIC_TMP
cp /proj/snic2022-X-YYY/nobackup/ref/hg19.fa* $SNIC_TMP/
 
# go to the $SNIC_TMP folder to make sure any temporary files
# are created there as well
cd $SNIC_TMP
 
# run the alignment using the index in $SNIC_TMP and the reads
# from project storage. write the sorted BAM containing
# alignments directly to $SNIC_TMP. Use 16 threads for
# alignment and 4 threads for sorting and compression, and
# 20GB RAM for sorting. These values are appropriate for a
# full standard rackham node.
bwa mem -t 16 $SNIC_TMP/hg19.fa /proj/snic2022-X-YYY/rawdata/sample.fq.gz | samtools sort -@ 4 -m 20G -O bam - > $SNIC_TMP/sample.bam
 
# copy the results back to the network file system
cp $SNIC_TMP/sample.bam /proj/snic2022-X-YYY/nobackup/results/

On using scratch