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
    - 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'
    - '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
    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
    mtnucratio:
        mtreads: 760
        mt_cov_avg: 770
        mt_nuc_ratio: 780
    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"