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

# Run only these modules
run_modules:
    - custom_content
    - fastqc
    - cutadapt
    - sortmerna
    - star
    - hisat2
    - rsem
    - salmon
    - samtools
    - picard
    - preseq
    - rseqc
    - qualimap
    - featureCounts

# Order of modules
top_modules:
    - 'fail_mapped_samples'
    - 'fail_strand_check'
    - 'featurecounts_deseq2_pca'
    - 'featurecounts_deseq2_clustering'
    - 'rsem_deseq2_pca'
    - 'rsem_deseq2_clustering'
    - 'salmon_deseq2_pca'
    - 'salmon_deseq2_clustering'
    - 'biotype_counts'
    - 'dupradar'

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'

# Move custom-content sections to the bottom of the report
report_section_order:
    software_versions:
        order: -1000
    nf-core-rnaseq-summary:
        order: -1100

# Don't show % Dups in the General Stats table (we have this from Picard)
table_columns_visible:
    FastQC:
        percent_duplicates: False

extra_fn_clean_exts:
    - '.ccurve'
    - '.hisat2'
    - '_2_val_2'
    - '_val_1'
    - '_duprate'
    - '.markdup'
    - '.read_distribution'
    - '.junction_annotation'
    - '.infer_experiment'
    - '.biotype'

# Customise the module search patterns to speed up execution time
#  - Skip module sub-tools that we are not interested in
#  - Replace file-content searching with filename pattern searching
#  - Don't add anything that is the same as the MultiQC default
# See https://multiqc.info/docs/#optimise-file-search-patterns for details
sp:
    cutadapt:
        fn: '*trimming_report.txt'

    sortmerna:
        fn: '*.sortmerna.log'

    hisat2:
        fn: '*.hisat2.summary.log'

    salmon/meta:
        fn: 'meta_info.json'

    preseq:
        fn: '*.ccurve.txt'

    featurecounts:
        fn: '*.summary'

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

    rseqc/bam_stat:
        fn: '*.bam_stat.txt'
    rseqc/gene_body_coverage:
        skip: true
    rseqc/junction_annotation:
        fn: '*.junction_annotation.log'
    rseqc/read_gc:
        skip: true
    rseqc/read_distribution:
        fn: '*.read_distribution.txt'
    rseqc/infer_experiment:
        fn: '*.infer_experiment.txt'

    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

# See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml
custom_data:
    fail_mapped_samples:
        section_name: 'WARNING: Fail Alignment Check'
        description: "List of samples that failed the STAR minimum mapped reads threshold specified via the '--min_mapped_reads' parameter, and hence were ignored for the downstream processing steps."
        plot_type: 'table'
        pconfig:
            id: 'fail_mapped_samples_table'
            table_title: 'Samples failed mapping threshold'
            namespace: 'Samples failed mapping threshold'
            format: '{:.2f}'
    fail_strand_check:
        section_name: 'WARNING: Fail Strand Check'
        description: "List of samples that failed the strandedness check between that provided in the samplesheet and calculated by the <a href='http://rseqc.sourceforge.net/#infer-experiment-py'>RSeQC infer_experiment.py</a> tool."
        plot_type: 'table'
        pconfig:
            id: 'fail_strand_check_table'
            table_title: 'Samples failed strandedness check'
            namespace: 'Samples failed strandedness check'
            format: '{:.2f}'
