with compressed input files output is gzipped twice

[AskPascal]

I did run cookiecutter remove on a set of paired reads in compressed fastq files like this:

$ cookiecutter remove -t 32 -1 81084_R1.1pct.cor.fq.gz -2 81084_R2.1pct.cor.fq.gz -f phix.txt -o .

The two output files are then gzipped twice:

$ gzip -cd 81084_R1.1pct.cor.fq.ok.fastq.gz | head

=> gibberish (gzipped binary)

$ gzip -cd 81084_R1.1pct.cor.fq.ok.fastq.gz | gzip -d | head

=> fastq