report_comment: >
    This report has been generated by the <a href="https://github.com/nf-core/atacseq" target="_blank">nf-core/atacseq</a>
    analysis pipeline. For information about how to interpret these results, please see the
    <a href="https://github.com/nf-core/atacseq/blob/master/docs/output.md" target="_blank">documentation</a>.

skip_generalstats: true

export_plots: true

fn_clean_exts:
    - 'fastq.gz'
    - '_trimmed'
    - '_val'
    - 'sorted.bam'
    - '.Lb'
    - 'mkD'
    - 'clN'
    - 'mLb'
    - 'mRp'

module_order:
    - fastqc:
        name: 'FastQC (library; raw)'
        info: 'This section of the report shows FastQC results before adapter trimming.'
        path_filters:
            - '*_fastqc.zip'
        path_filters_exclude:
            - '*val*_fastqc.zip'
            - '*trimmed_fastqc.zip'
    - cutadapt:
        name: 'cutadapt (library; trimmed)'
        info: 'This section of the report shows the length of trimmed reads by cutadapt.'
        path_filters:
            - '*_trimming_report.txt'
    - fastqc:
        name: 'FastQC (library; trimmed)'
        info: 'This section of the report shows FastQC results after adapter trimming.'
        path_filters:
            - '*val*_fastqc.zip'
            - '*trimmed_fastqc.zip'
    - samtools:
        name: 'SAMTools (library)'
        info: 'This section of the report shows SAMTools results for individual libraries.'
        path_filters:
            - '*.Lb.sorted.bam*'
    - samtools:
        name: 'SAMTools (merged library; unfiltered)'
        info: 'This section of the report shows SAMTools results after merging libraries and before filtering.'
        path_filters:
            - '*mLb.mkD.sorted.bam*'
    - samtools:
        name: 'SAMTools (merged library; filtered)'
        info: 'This section of the report shows SAMTools results after merging libraries and after filtering.'
        path_filters:
            - '*mLb.clN.sorted.bam*'
    - picard:
        name: 'Picard (merged library; filtered)'
        info: 'This section of the report shows picard results after merging libraries and after filtering.'
        path_filters:
            - '*mLb*'
    - samtools:
        name: 'SAMTools (merged replicate; filtered)'
        info: 'This section of the report shows SAMTools results after merging replicates and before filtering.'
        path_filters:
            - '*mRp.clN*'
    - picard:
        name: 'Picard (merged replicate; filtered)'
        info: 'This section of the report shows picard results after merging libraries and before filtering.'
        path_filters:
            - '*mRp.clN*'
    - featureCounts:
        name: 'featureCounts (merged library)'
        info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
        path_filters:
            - '*mLb.clN.featureCounts*'
    - featureCounts:
        name: 'featureCounts (merged replicate)'
        info: 'This section of the report shows featureCounts results for the number of reads assigned to merged replicate consensus peaks.'
        path_filters:
            - '*mRp.clN.featureCounts*'

report_section_order:
    mlib_peak_count:
        order: -1000
    mrep_peak_count:
        order: -1100
    mlib_frip_score:
        order: -1200
    mrep_frip_score:
        order: -1300
    mlib_peak_annotation:
        order: -1400
    mrep_peak_annotation:
        order: -1500
    mlib_deseq2_pca:
        order: -1600
    mrep_deseq2_pca:
        order: -1700
    mlib_deseq2_clustering:
        order: -1800
    mrep_deseq2_clustering:
        order: -1900
    software_versions:
        order: -2000
    nf-core-atacseq-summary:
        order: -2100

custom_plot_config:
    picard-insertsize:
        cpswitch_c_active: False
        smooth_points: 1000

    featurecounts:
        cpswitch_c_active: False

    featurecounts-1:
        cpswitch_c_active: False