Rewriting a for-loop to use it with "parallel" - bash

Question

I am trying to rewrite a for-loop (that works great) and run it as parallel but i having all sorts of problems. Here is my for loop
function no_sam {
filename=$(basename "$file")
extension="${file##*.}"
if [ $extension = "sam" ];
then
filename="${filename%.*}"
feat_out=$filename.out
htseq-count -f $types -r "$pos" -m "$mode" -i "$attribute" -s "$strand" -t "$feature" -a "$qual" "$file" "$input_gff" > "$feat_out"
grep -v "_" "$feat_out" > temp && mv temp "$feat_out"
mv "$feat_out" "$counts_folder"
elif [ $extension = "bam" ];
then
filename="${filename%.*}"
feat_out=$filename.out
htseq-count -f $types -r "$pos" -m "$mode" -i "$attribute" -s "$strand" -t "$feature" -a "$qual" "$file" "$input_gff" > "$feat_out"
grep -v "_" "$feat_out" > temp && mv temp "$feat_out"
mv "$feat_out" "$counts_folder"
fi
}
for file in "${multi[#]}"; do
no_sam
done
And when i replaced the for loop with GNU parallel, i am getting error
"${multi[#]}" no_sam | parallel
testfile.sam: command not found

Answer 1

Try this (based on https://www.gnu.org/software/parallel/man.html#EXAMPLE:-Using-shell-variables and https://www.gnu.org/software/parallel/man.html#EXAMPLE:-Calling-Bash-functions):
function no_sam {
file="$1"
filename=$(basename "$file")
extension="${file##*.}"
if [ $extension = "sam" ];
then
filename="${filename%.*}"
feat_out=$filename.out
htseq-count -f $types -r "$pos" -m "$mode" -i "$attribute" -s "$strand" -t "$feature" -a "$qual" "$file" "$input_gff" > "$feat_out"
grep -v "_" "$feat_out" > temp && mv temp "$feat_out"
mv "$feat_out" "$counts_folder"
elif [ $extension = "bam" ];
then
filename="${filename%.*}"
feat_out=$filename.out
htseq-count -f $types -r "$pos" -m "$mode" -i "$attribute" -s "$strand" -t "$feature" -a "$qual" "$file" "$input_gff" > "$feat_out"
grep -v "_" "$feat_out" > temp && mv temp "$feat_out"
mv "$feat_out" "$counts_folder"
fi
}
export -f no_sam
parallel no_sam ::: "${multi[#]}"
From the way you try to use GNU Parallel I think you will benefit from spending an hour walking through man parallel_tutorial.
Your command line will love you for it.