fastp PE read output bug

[colindaven]

• mm2 PE and SE deliver same output
• PE reads not listed properly in BAM or samtools flagstat of BAM
• R2 not passed to minimap2 aligner properly from trimming

@PG ID:minimap2 PN:minimap2 VN:2.21-r1071 CL:minimap2 -x sr -a --split-prefix /bla/tmp_sample3_R1.trm -t 16 /bla/metagenref/wochenende/2021_12_human_bact_arch_fungi_vir.fa /blabla/nf_wochenende/work/4a/ad46d170bc8d8f6bb46c0fe4ab2437/tmp_sample3_R1.trm.fastq

Edit: This was due to reads trimmed by fastp (PE reads) not being output correctly.

Workaround before bugfix: use the standard trimmer trimmomatic