Trimming paired-end reads does not write trimmed FASTQ files.

[ghuls]

Describe the bug
Trimming paired-end reads does not write trimmed FASTQ files, but only the HTML and JSON file.

To Reproduce

biofastq-a \
    --threads 2 \
    --trim \
    --output-dir fastq_cleaned/ \
    --in2 fastq/sample_R2.fastq.gz \
     fastq/sample_R1.fastq.gz

Expected behavior

I expect (trimmed) output FASTQ files for both R1 and R2 FASTQ files.
fastq_report.json

A clear and concise description of what you expected to happen.

ouptut

Content of fastq_cleaned/:

• sample_R1.fastq_report.html
• sample_R1.fastq_report.json

[DilaDeniz]

Fixed it and pushed to the experimental1 branch. The writer now opens correctly while computing the trim output path, just like with a single file path. I also added IsTerminal because forgetting the headless flag in non interactive environments like Docker was causing the process to hang or stop midway through writing the report. I'll also merge it to main