How to save outputs from current directory to another a directory in a shell script?

Question

I want to read all files in my current directory and would like to save the result on another directory. The code is below but could not get the files in the excepted directory. Does anyone can help me.

for file in *.sorted.bam
do 
samtools index "$file" -o "${file%.sort.bam}".bam | mv /mnt/d/Document/bt2Alignment_result
done

Thank you!

Answer 1

Here's a fixed version of your code:

for file in *.sorted.bam
do
    outfile="${file%.sorted.bam}.bam"
    samtools index "$filepath" -o "$outfile"
    mv "$outfile" /mnt/d/Document/bt2Alignment_result/
done

^{remark: you were using the glob *.sorted.bam while trying to strip the suffix .sort.bam}

---

That said, I don't think that you even need to mv the output file because samtools can directly create it where you want it to be (with the -o option). On a different note, sometimes it's convenient to specify a path in the glob, for example ./datadir/*.sorted.bam, so you should rather do:

for filepath in ./*.sorted.bam
do
    filename=${filepath##*/}
    outpath=/mnt/d/Document/bt2Alignment_result/"${filename%.sorted.bam}.bam"
    samtools index "$filepath" -o "$outpath"
done

Answer 2

Use mv in the next line with *.sorted.bam

for file in *.sorted.bam
do 
samtools index "$file" -o "${file%.sorted.bam}".bam 
mv *.sorted.bam /mnt/d/Document/bt2Alignment_result/
done