eager/assets/multiqc_config.yaml at 27d0d8710927ea29e949415a16e4d49f76935290 · nf-core/eager · GitHub

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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>.
top_modules:
     - 'fastqc':
        name: 'FastQC (pre-AdapterRemoval)'
        path_filters:
            - '*_raw_fastqc.zip'
     - 'fastp'
     - 'adapterRemoval'
     - 'fastqc':
        name: 'FastQC (post-AdapterRemoval)'
        path_filters:
            - '*.truncated_fastqc.zip'
            - '*.combined*_fastqc.zip'
     - 'samtools':
        name: 'Samtools Flagstat (pre-samtools filter)'
        path_filters:
             - '*.sorted.stats'
     - 'samtools':
        name: 'Samtools Flagstat (post-samtools filter)'
        path_filters:
             - '*.sorted.bam.filtered.stats'
     - 'dedup'
     - 'preseq'
     - 'qualimap'
     - 'damageprofiler'
     - 'gatk'
qualimap_config:
    general_stats_coverage:
        - 1
        - 2
        - 3
        - 4
        - 5
table_columns_visible:
    FastQC (pre-AdapterRemoval):
        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-AdapterRemoval):
        percent_duplicates: False
        total_sequences: True
        percent_gc: True
    Samtools Flagstat (pre-samtools filter):
        mapped_passed: True
    Samtools Flagstat (post-samtools filter):
        mapped_passed: True
    QualiMap:
        1_x_pc: True
        5_x_pc: True
        percentage_aligned: False
    DamageProfiler:
        3 Prime1: True
        3 Prime2: True
        5 Prime1: True
        5 Prime2: True
        mean_readlength: True
        median_readlength: True
table_columns_placement:
    FastQC (pre-AdapterRemoval):
        total_sequences: 100
        avg_sequence_length: 110
        percent_gc: 120
    fastp:
        after_filtering_gc_content: 200
    Adapter Removal:
        percent_aligned: 300
    FastQC (post-AdapterRemoval):
        total_sequences: 400
        avg_sequence_length: 410
        percent_gc: 420
    Samtools Flagstat (pre-samtools filter):
        mapped_passed: 500
    Samtools Flagstat (post-samtools filter):
        mapped_passed: 510
    DeDup:
        clusterfactor: 600
        duplication_rate: 610
    QualiMap:
        median_coverage: 700
        1_x_pc: 710
        2_x_pc: 720
        3_x_pc: 730
        4_x_pc: 740
        5_x_pc: 750
        avg_gc: 760
    mtnucratio:
        mtreads: 800
        mt_cov_avg: 810
        mt_nuc_ratio: 820
    DamageProfiler:
        3 Prime1: 900
        3 Prime2: 910
        5 Prime1: 920
        5 Prime2: 930
        mean_readlength: 940
        median_readlength: 950
read_count_multiplier: 1
read_count_prefix: ''
read_count_desc: ''
decimalPoint_format: '.'
thousandsSep_format: ','