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

export_plots: true

# Run only these modules
run_modules:
  - custom_content
  - fastqc
  - star
  - samtools
  - picard
  - gatk
  - snpeff
  - vep

# Order of modules
module_order:
  - fastqc:
      name: "FastQC (raw)"
      path_filters:
        - "*_val_*.zip"
  - star:
      name: "Read Alignment (STAR)"
  - samtools:
      name: "Samtools Flagstat"
  - picard:
      name: "GATK4 MarkDuplicates"
      info: "Metrics generated either by GATK4 MarkDuplicates"
  - qualimap:
      name: "Qualimap"
  - gatk:
      name: "GATK4 BQSR"
  - snpeff:
      name: "SNPeff"
  - vep:
      name: "VEP"

extra_fn_clean_exts:
  - "_val"

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

sp:
  samtools/stats:
    fn: "*.aligned.bam.stats"
  samtools/flagstat:
    fn: "*.aligned.bam.flagstat"
  picard/markdups:
    fn: "*.markdup.sorted.metrics"
  snpeff:
    contents: "SnpEff_version"
    max_filesize: 5000000
