report_comment: >
    This report has been generated by the <a href="https://bings.mssm.edu" target="_blank">BiNGS Core</a> RNA-Seq
    analysis pipeline. 

# Run only these modules
run_modules:
    - custom_content
    - fastqc
    - cutadapt
    - star
    - salmon
    - samtools
    - qualimap
    - featureCounts

module_order:
    - fastqc:
        name: 'FastQC (raw)'
        anchor: 'fastqc_raw'
        info: 'This section of the report shows FastQC results before adapter trimming.'
        path_filters:
            - '*/fastqc/*.zip'
    - cutadapt
    - fastqc:
        name: 'FastQC (trimmed)'
        anchor: 'fastqc_trimmed'
        info: 'This section of the report shows FastQC results after adapter trimming.'
        path_filters:
            - '*/trimgalore/*.zip'
    - star
    - samtools
    - qualimap
    - salmon
    - biotype_counts
    - deseq2_clustering
    - deseq2_pca_condition
    - deseq2_pca_sequencing_batch
    - sample_metadata_table

# Move custom-content sections to the bottom of the report
report_section_order:
    sample_metadata_table:
        order: 100
    general_stats:
        order: -1100
    fastqc_raw:
        order: -1200
    cutadapt:
        order: -1300
    fastqc_trimmed:
        order: -1400
    star:
        order: -1500
    Samtools:
        order: -1600
    biotype_counts:
        order: -1700
    featurecounts:
        order: -1800
    qualimap:
        order: -1900
    deseq2_pca_sequencing_batch:
        order: -2000
    deseq2_pca_condition:
        order: -2100
    deseq2_clustering:
        order: -2200
    salmon:
        order: -2300
    annotation_information:
        order: -2400
    software_versions:
        order: -2500

extra_fn_clean_exts:
    - '_val_1'
    - '_val_2'
    - '.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'
    
    salmon/meta:
        fn: 'meta_info.json'
    
    samtools/stats:
        fn: '*.stats'
    samtools/flagstat:
        fn: '*.flagstat'
    samtools/idxstats:
        fn: '*.idxstats*'
