Atropos generated empty gzip files are not proper gzip file

[jganbat-fn]

When given 2 empty R1 and R2 fastq files, Atropos does generate 2 output files. Unfortunately if we specify it as .gz file it is actually not a proper gzip file. It is related to this issue fix: https://github.com/jdidion/atropos/issues/122

Atropos version 1.1.29

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

When attempt to use gzip or zcat I get the following

 % gunzip test_R1.trimmed.fastq.gz

gzip: empty.trim.fastq.gz: unexpected end of file

[jdidion]

Fixed - will be in the next release

[jganbat-fn]

Fixed - will be in the next release

Great, thank you very much 😄

[jdidion]

Please try release 1.1.31