report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/taxprofiler" target="_blank">nf-core/taxprofiler</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/taxprofiler" target="_blank">documentation</a>.
report_section_order:
  "nf-core-taxprofiler-methods-description":
    order: -1000
  software_versions:
    order: -1001
  "nf-core-taxprofiler-summary":
    order: -1002

export_plots: true

custom_logo: "nf-core-taxprofiler_logo_custom_light.png"
custom_logo_url: https://nf-co.re/taxprofiler
custom_logo_title: "nf-core/taxprofiler"

run_modules:
  - fastqc
  - adapterRemoval
  - bbduk
  - prinseqplusplus
  - fastp
  - filtlong
  - bowtie2
  - minimap2
  - samtools
  - kraken
  - kaiju
  - metaphlan
  - diamond
  - malt
  - motus
  - porechop
  - custom_content

#extra_fn_clean_exts:
#    - '_fastp'
#    - '.pe.settings'
#    - '.se.settings'

top_modules:
  - "fastqc":
      name: "FastQC (pre-Trimming)"
      path_filters:
        - "*raw_*fastqc.zip"
  - "fastqc":
      name: "Falco (pre-Trimming)"
      path_filters:
        - "*_raw_falco_*_report.html"
  - "fastp"
  - "adapterRemoval"
  - "porechop"
  - "fastqc":
      name: "FastQC (post-Trimming)"
      path_filters:
        - "*_processed_*fastqc.zip"
  - "fastqc":
      name: "Falco (post-Trimming)"
      path_filters:
        - "*_processed_falco_*_report.html"
  - "bbduk"
  - "prinseqplusplus"
  - "filtlong"
  - "bowtie2":
      name: "bowtie2"
  - "samtools":
      name: "Samtools Stats"
  - "kraken":
      name: "Kraken"
      path_filters:
        - "*.kraken2.kraken2.report.txt"
  - "kraken":
      name: "Bracken"
      anchor: "bracken"
      target: "Bracken"
      doi: "10.7717/peerj-cs.104"
      info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
      extra: "Note: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
      path_filters:
        - "*.bracken.kraken2.report.txt"
  - "kraken":
      name: "Centrifuge"
      anchor: "centrifuge"
      target: "Centrifuge"
      doi: "10.1101/gr.210641.116"
      info: "is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. Note: Figure title"
      extra: "Note: plot title will say Kraken2 due to Centrifuge producing the same output format as Kraken. If activated, see the actual Kraken2 results in the section above."
      path_filters:
        - "*.centrifuge.txt"
  - "malt":
      name: "MALT"
  - "diamond"
  - "kaiju":
      name: "Kaiju"
  - "motus"

#It is not possible to set placement for custom kraken and centrifuge columns.

table_columns_placement:
  FastQC (pre-Trimming):
    total_sequences: 100
    avg_sequence_length: 110
    percent_duplicates: 120
    percent_gc: 130
    percent_fails: 140
  Falco (pre-Trimming):
    total_sequences: 200
    avg_sequence_length: 210
    percent_duplicates: 220
    percent_gc: 230
    percent_fails: 240
  fastp:
    pct_adapter: 300
    pct_surviving: 310
    pct_duplication: 320
    after_filtering_gc_content: 330
    after_filtering_q30_rate: 340
    after_filtering_q30_bases: 350
  Adapter Removal:
    aligned_total: 360
    percent_aligned: 370
    percent_collapsed: 380
    percent_discarded: 390
  FastQC (post-Trimming):
    total_sequences: 400
    avg_sequence_length: 410
    percent_duplicates: 420
    percent_gc: 430
    percent_fails: 440
  Falco (post-Trimming):
    total_sequences: 500
    avg_sequence_length: 510
    percent_duplicates: 520
    percent_gc: 530
    percent_fails: 540
  bowtie2:
    overall_alignment_rate: 600
  Samtools Stats:
    raw_total_sequences: 700
    reads_mapped: 710
    reads_mapped_percent: 720
    reads_properly_paired_percent: 730
    non-primary_alignments: 740
    reads_MQ0_percent: 750
    error_rate: 760
  MALT:
    Num. of queries: 1000
    Total reads: 1100
    Mappability: 1200
    Assig. Taxonomy: 1300
    Taxonomic assignment success: 1400
  Kaiju:
    assigned: 2000
    "% Assigned": 2100
    "% Unclassified": 2200

table_columns_visible:
  FastQC (pre-Trimming):
    total_sequences: True
    avg_sequence_length: True
    percent_duplicates: True
    percent_gc: True
    percent_fails: False
  Falco (pre-Trimming):
    total_sequences: True
    avg_sequence_length: True
    percent_duplicates: True
    percent_gc: True
    percent_fails: False
  fastp:
    pct_adapter: True
    pct_surviving: True
    pct_duplication: False
    after_filtering_gc_content: False
    after_filtering_q30_rate: False
    after_filtering_q30_bases: False
  Adapter Removal:
    aligned_total: True
    percent_aligned: True
    percent_collapsed: True
    percent_discarded: False
  FastQC (post-Trimming):
    total_sequences: True
    avg_sequence_length: True
    percent_duplicates: False
    percent_gc: False
    percent_fails: False
  Falco (post-Trimming):
    total_sequences: True
    avg_sequence_length: True
    percent_duplicates: False
    percent_gc: False
    percent_fails: False
  bowtie2:
    overall_alignment_rate: True
  Samtools Stats:
    raw_total_sequences: True
    reads_mapped: True
    reads_mapped_percent: True
    reads_properly_paired_percent: False
    non-primary_alignments: False
    reads_MQ0_percent: False
    error_rate: False
  Kraken:
    "% Unclassified": True
    "% Top 5": False
  Bracken:
    "% Unclassified": True
    "% Top 5": False
  Centrifuge:
    "% Unclassified": True
    "% Top 5": False
  MALT:
    Num. of queries: True
    Total reads: True
    Mappability: True
    Assig. Taxonomy: False
    Taxonomic assignment success: True
  Kaiju:
    assigned: False
    "% Assigned": False
    "% Unclassified": True
table_columns_name:
  FastQC (pre-Trimming):
    total_sequences: "Nr. Input Reads"
    avg_sequence_length: "Length Input Reads"
    percent_gc: "% GC Input Reads"
    percent_duplicates: "% Dups Input Reads"
    percent_fails: "% Failed Input Reads"
  Falco (pre-Trimming):
    total_sequences: "Nr. Input Reads"
    avg_sequence_length: "Length Input Reads"
    percent_gc: "% GC Input Reads"
    percent_duplicates: "% Dups Input Reads"
    percent_fails: "% Failed Input Reads"
  FastQC (post-Trimming):
    total_sequences: "Nr. Processed Reads"
    avg_sequence_length: "Length Processed Reads"
    percent_gc: "% GC Processed Reads"
    percent_duplicates: "% Dups Processed Reads"
    percent_fails: "% Failed Processed Reads"
  Falco (post-Trimming):
    total_sequences: "Nr. Processed Reads"
    avg_sequence_length: "Length Processed Reads"
    percent_gc: "% GC Processed Reads"
    percent_duplicates: "% Dups Processed Reads"
    percent_fails: "% Failed Processed Reads"
  Samtools Stats:
    raw_total_sequences: "Nr. Reads Into Mapping"
    reads_mapped: "Nr. Mapped Reads"
    reads_mapped_percent: "% Mapped Reads"

extra_fn_clean_exts:
  - ".kraken2.kraken2.report.txt"
  - ".centrifuge.txt"
  - ".bracken.kraken2.report.txt"
  - ".settings"