report_comment: >
    This report has been generated by the <a href="https://github.com/nf-core/cutandrun" target="_blank">nf-core/cutandrun</a>
    analysis pipeline. For information about how to interpret these results, please see the
    <a href="https://nf-co.re/cutandrun" target="_blank">documentation</a>.
report_section_order:
    software_versions:
        order: -1000
    nf-core-cutandrun-summary:
        order: -1001

export_plots: true

report_header_info:
  - Application Type: "CUT&RUN"

# Run only these modules
run_modules:
    - custom_content
    - fastqc
    - cutadapt
    - bowtie2
    - samtools
    - picard

module_order:
    - fastqc:
        name: 'FastQC (raw)'
        info: 'This section of the report shows FastQC results before adapter trimming.'
        path_filters:
            - './fastqc/*.zip'
    - cutadapt
    - fastqc:
        name: 'FastQC (trimmed)'
        info: 'This section of the report shows FastQC results after adapter trimming.'
        path_filters:
            - './trimgalore/fastqc/*.zip'
    - bowtie2:
        name: 'Bowtie2 (target)'
        path_filters:
            - "./bowtie2/*target.bowtie2.log"
    - bowtie2:
        name: 'Bowtie2 (spike-in)'
        path_filters:
            - "./bowtie2/*spikein.bowtie2.log"
    - samtools
    - picard
    - custom_content

custom_content:
  order:
    - fragment_lengths
    - software_versions
    - software_versions_unique
extra_fn_clean_exts:
    - '_val_1'
    - '_val_2'
# Don't show % Dups in the General Stats table (we have this from Picard)
table_columns_visible:
    FastQC:
        percent_duplicates: False

section_comments:
    fastqc_raw_fastqc_per_base_sequence_content: >
        The discordant sequence content at the begining of the reads are common phenomenon for CUT&TAG reads. Failing to pass the Per base seuqnence content does not mean your data failed.
        - It can be due to the Tn5 preference.
        - What you might be detecting is the 10-bp periodicity that shows up as a sawtooth pattern in the length distribution. If so, this is normal and will not affect alignment or peak calling. In any case we do not recommend trimming as the bowtie2 parameters that we list will give accurate mapping information without trimming.

# Customise the module search patterns to speed up execution time
sp:
    cutadapt:
        fn: '*trimming_report.txt'

    samtools/stats:
        fn: '*.stats'
    samtools/flagstat:
        fn: '*.flagstat'
    samtools/idxstats:
        fn: '*.idxstats*'

    picard/markdups:
        fn: '*.MarkDuplicates.metrics.txt'
    picard/alignment_metrics:
        skip: true
    picard/basedistributionbycycle:
        skip: true
    picard/gcbias:
        skip: true
    picard/hsmetrics:
        skip: true
    picard/insertsize:
        skip: true
    picard/oxogmetrics:
        skip: true
    picard/pcr_metrics:
        skip: true
    picard/quality_by_cycle:
        skip: true
    picard/quality_score_distribution:
        skip: true
    picard/quality_yield_metrics:
        skip: true
    picard/rnaseqmetrics:
        skip: true
    picard/rrbs_metrics:
        skip: true
    picard/sam_file_validation:
        skip: true
    picard/variant_calling_metrics:
        skip: true
    picard/wgs_metrics:
        skip: true
