Atropos trim multi thread stuck in infinite loop on empty files.

[jganbat-fn]

When given 2 empty R1 and R2 fastq files with multi-thread enabled causes it to stuck on waiting forever.

Atropos version 1.1.28

Here is the bash script to replicate it,

test_R1.fastq.gz and test_R2.fastq.gz are empty files.

FQ1=test_R1.fastq.gz
FQ2=test_R2.fastq.gz
TFQ1=${FQ1%%.fastq.gz}.trimmed.fastq.gz
TFQ2=${FQ2%%.fastq.gz}.trimmed.fastq.gz
CORE="-T 4"

atropos trim $CORE \
    --preserve-order \
    --no-default-adapters \
    -a <ANY ADAPTER> \
    -A <ANY ADAPTER> \
    -pe1 $FQ1 -pe2 $FQ2 -o $TFQ1 -p $TFQ2

[jdidion]

Thanks - will get a fix for this out shortly

[jdidion]

Fixed in 1.1.29