custom_logo: "nf-core-molkart_logo_light.png"
custom_logo_url: https://github.com/nf-core/molkart/
custom_logo_title: "nf-core/molkart"

report_comment: >
  This report has been generated by the <a href="https://github.com/nf-core/molkart/releases/tag/1.0.0" target="_blank">nf-core/molkart</a>
  analysis pipeline. For information about how to interpret these results, please see the
  <a href="https://nf-co.re/molkart/1.0.0/docs/output" target="_blank">documentation</a>.
report_section_order:
  "nf-core-molkart-methods-description":
    order: -1000
  software_versions:
    order: -1001
  "nf-core-molkart-summary":
    order: -1002

export_plots: true

custom_data:
  my_custom_content_image:
    section_name: "Crop overview"
  segmentation_stats:
    id: "segmentation_stats"
    section_name: "QC statistics from segmentation"
    pconfig:
      id: "segmentation_stats_table"
      namespace: "Segmentation stats"
    headers:
      segmentation_method:
        title: Segmentation method
        description: "Segmentation method"
      total_cells:
        title: Total Number of cells
        description: "Total # cells"
      avg_area:
        title: Average cell area
        description: "Average area per cell"
      total_spots:
        title: Total number of spots
        description: "Average number of spots assigned per cell"
      spot_assign_per_cell:
        title: Average spots assigned per cell
        description: "Average number of spots assigned per cell"
      spot_assign_total:
        title: Total spots assigned
        description: "Total number of spots assigned"
      spot_assign_percent:
        title: Percentage of spots assigned to cell
        description: "% of spots assigned to cells"
      duplicated_total:
        title: Total number of duplicated spots in the area
        description: "Total number of duplicated spots"
      labels_total:
        title: Total number of cells before filtering
        description: "Total number of segmented labels"
      labels_below_thresh:
        title: Number of removed small cells
        description: "Total number of labels below min_area"
      labels_above_thresh:
        title: Number of removed large cells
        description: "Total number of labels above max_area"
sp:
  segmentation_stats:
    fn: "final_QC.all_samples.csv"
    shared: true
  my_custom_content_image:
    fn: "*.png"
ignore_images: false
