custom_logo: "nf-core_eager_logo_outline_drop.png"
custom_logo_url: https://github.com/nf-core/eager/
custom_logo_title: "nf-core/eager"

report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/eager" target="_blank">nf-core/eager</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://github.com/nf-core/eager" target="_blank">documentation</a>.
run_modules:
  - adapterRemoval
  - bowtie2
  - custom_content
  - damageprofiler
  - dedup
  - fastp
  - fastqc
  - gatk
  - kraken
  - malt
  - mapdamage
  - mtnucratio
  - multivcfanalyzer
  - picard
  - preseq
  - qualimap
  - samtools
  - sexdeterrmine
  - hops
  - bcftools

extra_fn_clean_exts:
  - "_fastp"
  - ".pe.settings"
  - ".se.settings"
  - ".settings"
  - ".pe.combined"
  - ".se.truncated"
  - ".mapped"
  - ".mapped_rmdup"
  - ".mapped_rmdup_stats"
  - "_libmerged_rg_rmdup"
  - "_libmerged_rg_rmdup_stats"
  - "_postfilterflagstat.stats"
  - "_flagstat.stat"
  - ".filtered"
  - ".filtered_rmdup"
  - ".filtered_rmdup_stats"
  - "_libmerged_rg_add"
  - "_libmerged_rg_add_stats"
  - "_rmdup"
  - ".unmapped"
  - ".fastq.gz"
  - ".fastq"
  - ".fq.gz"
  - ".fq"
  - ".bam"
  - ".kreport"
  - ".unifiedgenotyper"
  - ".trimmed_stats"
  - "_libmerged"
  - "_bt2"

top_modules:
  - "fastqc":
      name: "FastQC (pre-Trimming)"
      path_filters:
        - "*_raw_fastqc.zip"
  - "fastp"
  - "adapterRemoval"
  - "fastqc":
      name: "FastQC (post-Trimming)"
      path_filters:
        - "*.truncated_fastqc.zip"
        - "*.combined*_fastqc.zip"
  - "bowtie2":
      path_filters:
        - "*_bt2.log"
  - "malt"
  - "hops"
  - "kraken"
  - "samtools":
      name: "Samtools Flagstat (pre-samtools filter)"
      path_filters:
        - "*_flagstat.stats"
  - "samtools":
      name: "Samtools Flagstat (post-samtools filter)"
      path_filters:
        - "*_postfilterflagstat.stats"
  - "dedup"
  - "picard"
  - "preseq":
      path_filters:
        - "*.preseq"
  - "damageprofiler"
  - "mapdamage"
  - "mtnucratio"
  - "qualimap"
  - "sexdeterrmine"
  - "bcftools"
  - "multivcfanalyzer":
      path_filters:
        - "*MultiVCFAnalyzer.json"
qualimap_config:
  general_stats_coverage:
    - 1
    - 2
    - 3
    - 4
    - 5

remove_sections:
  - sexdeterrmine-snps

table_columns_visible:
  FastQC (pre-Trimming):
    percent_duplicates: False
    percent_gc: True
    avg_sequence_length: True
  fastp:
    pct_duplication: False
    after_filtering_gc_content: True
    pct_surviving: False
  Adapter Removal:
    aligned_total: False
    percent_aligned: True
  FastQC (post-Trimming):
    avg_sequence_length: True
    percent_duplicates: False
    total_sequences: True
    percent_gc: True
  bowtie2:
    overall_alignment_rate: True
  MALT:
    Taxonomic assignment success: False
    Assig. Taxonomy: False
    Mappability: True
    Total reads: False
    Num. of queries: False
  Kraken:
    "% Unclassified": True
    "% Top 5": False
  Samtools Flagstat (pre-samtools filter):
    flagstat_total: True
    mapped_passed: True
  Samtools Flagstat (post-samtools filter):
    mapped_passed: True
  DeDup:
    dup_rate: False
    clusterfactor: True
    mapped_after_dedup: True
  Picard:
    PERCENT_DUPLICATION: True
  DamageProfiler:
    5 Prime1: True
    5 Prime2: True
    3 Prime1: False
    3 Prime2: False
    mean_readlength: True
    median: True
  mapDamage:
    5 Prime1: True
    5 Prime2: True
    3 Prime1: False
    3 Prime2: False
  mtnucratio:
    mt_nuc_ratio: True
  QualiMap:
    mapped_reads: True
    mean_coverage: True
    1_x_pc: True
    5_x_pc: True
    percentage_aligned: False
    median_insert_size: False
  MultiVCFAnalyzer:
    Heterozygous SNP alleles (percent): True
  endorSpy:
    endogenous_dna: True
    endogenous_dna_post: True
  nuclear_contamination:
    Num_SNPs: True
    Method1_MOM_estimate: False
    Method1_MOM_SE: False
    Method1_ML_estimate: True
    Method1_ML_SE: True
    Method2_MOM_estimate: False
    Method2_MOM_SE: False
    Method2_ML_estimate: False
    Method2_ML_SE: False
  snp_coverage:
    Covered_Snps: True
    Total_Snps: False

table_columns_placement:
  FastQC (pre-Trimming):
    total_sequences: 100
    avg_sequence_length: 110
    percent_gc: 120
  fastp:
    after_filtering_gc_content: 200
  Adapter Removal:
    percent_aligned: 300
  FastQC (post-Trimming):
    total_sequences: 400
    avg_sequence_length: 410
    percent_gc: 420
  Bowtie 2 / HiSAT2:
    overall_alignment_rate: 450
  MALT:
    Num. of queries: 430
    Total reads: 440
    Mappability: 450
    Assig. Taxonomy: 460
    Taxonomic assignment success: 470
  Kraken:
    "% Unclassified": 480
  Samtools Flagstat (pre-samtools filter):
    flagstat_total: 551
    mapped_passed: 552
  Samtools Flagstat (post-samtools filter):
    flagstat_total: 600
    mapped_passed: 620
  endorSpy:
    endogenous_dna: 610
    endogenous_dna_post: 640
  nuclear_contamination:
    Num_SNPs: 1100
    Method1_MOM_estimate: 1110
    Method1_MOM_SE: 1120
    Method1_ML_estimate: 1130
    Method1_ML_SE: 1140
    Method2_MOM_estimate: 1150
    Method2_MOM_SE: 1160
    Method2_ML_estimate: 1170
    Method2_ML_SE: 1180
  snp_coverage:
    Covered_Snps: 1050
    Total_Snps: 1060
  DeDup:
    mapped_after_dedup: 620
    clusterfactor: 630
  Picard:
    PERCENT_DUPLICATION: 650
  DamageProfiler:
    5 Prime1: 700
    5 Prime2: 710
    3 Prime1: 720
    3 Prime2: 730
    mean_readlength: 740
    median: 750
  mapDamage:
    5 Prime1: 760
    5 Prime2: 765
    3 Prime1: 770
    3 Prime2: 775
  mtnucratio:
    mtreads: 780
    mt_cov_avg: 785
    mt_nuc_ratio: 790
  QualiMap:
    mapped_reads: 800
    mean_coverage: 805
    median_coverage: 810
    1_x_pc: 820
    2_x_pc: 830
    3_x_pc: 840
    4_x_pc: 850
    5_x_pc: 860
    avg_gc: 870
  sexdeterrmine:
    RateX: 1000
    RateY: 1010
  MultiVCFAnalyzer:
    Heterozygous SNP alleles (percent): 1200
read_count_multiplier: 1
read_count_prefix: ""
read_count_desc: ""
ancient_read_count_prefix: ""
ancient_read_count_desc: ""
ancient_read_count_multiplier: 1
decimalPoint_format: "."
thousandsSep_format: ","
report_section_order:
  software_versions:
    order: -1000
  nf-core-eager-summary:
    order: -1001
export_plots: 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"
  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"
  Samtools Flagstat (pre-samtools filter):
    flagstat_total: "Nr. Reads Into Mapping"
    mapped_passed: "Nr. Mapped Reads"
  Samtools Flagstat (post-samtools filter):
    flagstat_total: "Nr. Mapped Reads Post-Filter"
    mapped_passed: "Nr. Mapped Reads Passed Post-Filter"
  Endogenous DNA Post (%):
    endogenous_dna_post (%): "Endogenous DNA Post-Filter (%)"
  Picard:
    PERCENT_DUPLICATION: "% Dup. Mapped Reads"
  DamageProfiler:
    mean_readlength: "Mean Length Mapped Reads"
    median_readlength: "Median Length Mapped Reads"
  QualiMap:
    mapped_reads: "Nr. Dedup. Mapped Reads"
    total_reads: "Nr. Dedup. Total Reads"
    avg_gc: "% GC Dedup. Mapped Reads"
  Bcftools Stats:
    number_of_records: "Nr. Overall Variants"
    number_of_SNPs: "Nr. SNPs"
    number_of_indels: "Nr. InDels"
  MALT:
    Mappability: "% Metagenomic Mappability"
  SexDetErrmine:
    RateErrX: "SexDet Err X Chr"
    RateErrY: "SexDet Err Y Chr"
    RateX: "SexDet Rate X Chr"
    RateY: "SexDet Rate Y Chr"
  custom_table_header_config:
    general_stats_table:
      median_coverage:
        format: "{:,.3f}"
      mean_coverage:
        format: "{:,.3f}"
