@botellaflotante I think @thermokarst’s advice to use cutadapt directly is the best way to accomplish this.
But I just want to share what I’ve done in the past to quickly split apart interleaved fastq files, in case this serves as a useful backup, or perhaps some inspiration to learn how to use
grep '@.*\.1\.1' -A 3 path-to-interleaved-seqs.fastq | grep -v '^--$' > forward-seqs.fastq
grep '@.*\.1\.2' -A 3 path-to-interleaved-seqs.fastq | grep -v '^--$' > reverse-seqs.fastq
grep grabs headers indicating forward/reverse, and the following 3 lines
grep eliminates spacer lines (which grep inserts when the
-A option is used)