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

export_plots: true

fn_clean_exts:
    - 'fastq.gz'
    - '_trimmed'
    - '_val'
    - 'sorted.bam'
    - '.Lb'
    - 'mkD'
    - 'clN'
    - 'mLb'
    - '_peaks'
    - '_spp'
    - '.spp'

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*'
    - preseq:
        name: 'Preseq (merged library; unfiltered)'
        info: 'This section of the report shows Preseq results after merging libraries and before filtering.'
        path_filters:
            - '*mLb*'
    - 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*'
    - deeptools:
        name: 'deepTools'
        info: 'This section of the report shows ChIP-seq QC plots generated by deepTools.'
        path_filters:
            - '*.plot*'
    - featureCounts:
        name: 'featureCounts'
        info: 'This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks.'
        path_filters:
            - '*featureCounts*'

report_section_order:
    peak_count:
        order: -1000
    frip_score:
        order: -1100
    strand_shift_correlation:
        order: -1200
    nsc_coefficient:
        order: -1300
    rsc_coefficient:
        order: -1400
    peak_annotation:
        order: -1500
    deseq2_pca_1:
        order: -1600
    deseq2_pca_2:
        order: -1700
    deseq2_pca_3:
        order: -1800
    deseq2_pca_4:
        order: -1900
    deseq2_pca_5:
        order: -2000
    deseq2_pca_6:
        order: -2100
    deseq2_pca_7:
        order: -2200
    deseq2_pca_8:
        order: -2300
    deseq2_pca_9:
        order: -2400
    deseq2_pca_10:
        order: -2500
    deseq2_clustering_1:
        order: -2600
    deseq2_clustering_2:
        order: -2700
    deseq2_clustering_3:
        order: -2800
    deseq2_clustering_4:
        order: -2900
    deseq2_clustering_5:
        order: -3000
    deseq2_clustering_6:
        order: -3100
    deseq2_clustering_7:
        order: -3200
    deseq2_clustering_8:
        order: -3300
    deseq2_clustering_9:
        order: -3400
    deseq2_clustering_10:
        order: -3500
    software_versions:
        order: -3600
    nf-core-chipseq-summary:
        order: -3700

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

    featurecounts:
        cpswitch_c_active: False
