the statement if [ -s "${line}*.fastq" ]; then echo .... seems always false.
The "" quotes seem to preserve the literal value of asterisk.
I found a workaround with just applying the exact regex but I would like to know if there is another, easier/faster way.
my workaround:
while IFS= read -r line; do
echo "Now downloading "${line}"\n"
docker run --rm -v "$(pwd)":/data -w /data inutano/sra-toolkit fasterq-dump "${line}" -t /data/shm -e $Processors
if [[ -s ${line}_1.fastq ]]; then
echo "Using pigz on ${line}.fastq"
pigz --best ${line}*.fastq
elif [[ -s ${line}.fastq ]]; then
pigz --best ${line}*.fastq
else
echo "${line}.fastq not found"
fi
done < "$INPUT_txt"
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