Parameters set for pb-16S-nf pipeline for PacBio HiFi 16S
    =========================================================
    Number of samples in samples TSV: 60
    Filter input reads above Q: 20
    Trim primers with cutadapt: Yes
    Limit to N reads if exceeding N reads (0 = disabled): 0
    Forward primer: AGRGTTYGATYMTGGCTCAG
    Reverse primer: AAGTCGTAACAAGGTARCY
    Minimum amplicon length filtered in DADA2: 1000
    Maximum amplicon length filtered in DADA2: 1600
    Using specified FASTQ for DADA2 error model: false
    DADA2 OMEGA_C parameter (default 1e-40): 1e-40
    maxEE parameter for DADA2 filterAndTrim: 5
    minQ parameter for DADA2 filterAndTrim: 0
    Pooling method for DADA2 denoise process: pseudo
    Minimum number of samples required to keep any ASV: 1
    Minimum number of reads required to keep any ASV: 5 
    Taxonomy sequence database for VSEARCH: /media/xiangyang/HiFi-16S-workflow/databases/silva-138-99-seqs.qza
    Taxonomy annotation database for VSEARCH: /media/xiangyang/HiFi-16S-workflow/databases/silva-138-99-tax.qza
    Skip Naive Bayes classification: true
    SILVA database for Naive Bayes classifier: /media/xiangyang/HiFi-16S-workflow/databases/silva_nr99_v138.2_toSpecies_trainset.fa.gz
    GTDB database for Naive Bayes classifier: /media/xiangyang/HiFi-16S-workflow/databases/GTDB_bac120_arc53_ssu_r220_fullTaxo.fa.gz
    GreenGenes2 database for Naive Bayes classifier: /media/xiangyang/HiFi-16S-workflow/databases/gg2_2024_09_toSpecies_trainset.fa.gz
    Database to prioritize for Naive Bayes classifier: Silva
    VSEARCH maxreject: 100
    VSEARCH maxaccept: 100
    VSEARCH perc-identity: 0.97
    QIIME 2 rarefaction curve sampling depth: null
    Number of threads specified for cutadapt: 184
    Number of threads specified for DADA2: 184
    Number of threads specified for VSEARCH: 184
    Script location for HTML report generation: /media/xiangyang/HiFi-16S-workflow/scripts/visualize_biom.Rmd
    Container enabled via docker/singularity: true
    Version of Nextflow pipeline: 0.9