Wrong results without error if saved_trimmed = true

[panzhang666666]

Description of the bug

Hi, I find a wired thing that if saved_trimmed = true used when I using fastp as trimmer, the mapped reads reduced a lot. Take OMICS_356_21 as an example, the M reads goes from 100.6M to 64.7M if I set saved_trimmed to true without any other parameter change. And both 2 pipeline finished successfully with " [main] INFO nextflow.Nextflow - -[nf-core/rnaseq] Pipeline completed successfully -". Does anyone know why？

Many thanks

Command used and terminal output

Read trimming options
trimmer : fastp
extra_fastp_args : --length_required 50 --cut_by_quality3 3 --cut_by_quality5 3 --cut_window_size 4 --cut_mean_quality 15

Alignment options
min_mapped_reads : 5

Quality Control
rseqc_modules : inner_distance,read_distribution

Process skipping options
skip_umi_extract : true
skip_pseudo_alignment: true
skip_markduplicates : true
skip_bigwig : true
skip_stringtie : true
skip_dupradar : true
skip_qualimap : true
skip_biotype_qc : true

Relevant files

No response

System information

No response