Hi all, I noticed in the documentation that in the Usage tab a warning that states to use the --skip-fastq parameter to avoid trimming the adapters before using umi-tools extract. I am confused, though, because according to the introduction the optional UMI extraction and miRNA adapter trimming (1.2) happens prior to the fastp adapter trimming step (1.3). Is it necessary to skip fastp, then? I may be misunderstanding. I am trying to do an analysis on data from a QIAseq kit. I am putting my current command here, in case that is helpful.

nextflow run nf-core/smrnaseq \
    -name "smrnaseq_${BASENAME}_${SLURM_JOB_ID}" \
    -profile singularity \
    --input ${SAMPLESHEET} \
    --outdir ${RESULTS_DIR} \
    --genome ${GENOME} \
    --mirtrace_species hsa \
    --with_umi true \
    --umitools_extract_method regex \
    --umitools_bc_pattern '.+(?P<discard_1>AACTGTAGGCACCATCAAT){s<=2}(?P<umi_1>.{12})(?P<discard_2>.+)' \
    --protocol qiaseq \
    --skip_mirdeep false \
    --max_cpus 16 \
    --max_memory 50.GB \
    --skip_fastp \
    -w ${WORK_DIR} \
    -resume