Mapping multiples

Question

[assane.mbodj]

Hi, I am coming to you for help. I am doing a mapping on short and long read files with BWA and MINIMAP2 My problem is that, I want to make an if loop that would allow me to choose either BWA if I work with short reads or MINIMAP2 for long reads on a single script

Here is the script I made in bash for the moment thanks in advance.

for R1 in ${DATA_DIR}/*_R1.fq.gz
do

R2=$(echo ${R1} | sed "s/R1.fq.gz/R2.fq.gz/g")
OUT=$(basename $R1 | awk -F "_" '{print $1}')

#mapping and sort bam file

        $BWA/bwa mem $GENOME $R1 $R2 > $Bam_file/$OUT.sam

    $Minimap --MD -t 4 -ax map-ont $GENOME $R1 $R2 > $Bam_file/$OUT.sam

    $samtools view -bS $Bam_file/$OUT.sam > $Bam_file/$OUT.bam

    $samtools sort $Bam_file/$OUT.bam -o $Bam_file/$OUT.sorted.bam

    $samtools index $Bam_file/$OUT.sorted.bam

done