Full Report

Date and Time: {{ date_time }}

Mode: {{ mode }}

Configuration Details

{% if config.DATA is defined %}

Data

    {% if config.DATA.assembly is defined %}
  • Assembly input: {{ config.DATA.assembly }}
  • Library: {{ config.DATA.library }}
  • {% else %} Nanopore:
  • {{ config.DATA.ORIGINAL.nanopore }}
  • {{ config.DATA.MOVED.nanopore }}
  • Pacbio:
  • {{ config.DATA.ORIGINAL.pacbio }}
  • {{ config.DATA.MOVED.pacbio }}
  • {% endif %}
{% endif %} {% if config.ALL_CHROMOSOMES is defined %}

Chromosomes

    {% for chromosome in config.ALL_CHROMOSOMES %}
  • {{ chromosome }}
  • {% endfor %}
{% endif %} {% if config.HAPLOTYPES is defined %}

Haplotypes

    {% for haplotype in config.HAPLOTYPES %}
  • {{ haplotype }}
  • {% endfor %}
{% endif %} {% if config.BUSCO_DATASET is defined %}

BUSCO Dataset

  • {{ config.BUSCO_DATASET }}
{% endif %} {% if config.ASSEMBLY_CHROMOSOMES is defined %}

Assembly Chromosomes

    {% for assembly_chromosome in config.ASSEMBLY_CHROMOSOMES %}
  • {{ assembly_chromosome }}
  • {% endfor %}
{% endif %} {% if config.SPECIES is defined %}

Species

  • Name: {{ config.SPECIES.name }}
  • {% if config.SPECIES.genome is defined %}
  • Genome: {{ config.SPECIES.genome }}
  • {% endif %}
  • Cell: {{ config.SPECIES.cell }}
{% endif %} {% if config.FLANKING_GENES is defined %}

Flanking Genes

    {% for gene in config.FLANKING_GENES %}
  • {{ gene }}
  • {% endfor %}
{% endif %} {% if config.RSS_LAYOUT is defined %}

RSS Extraction

    {% for gene, rss_types in config.RSS_LAYOUT.items() %}
  • {{ gene }}
      {% for rss_type, orientations in rss_types.items() %}
    • {{ rss_type }}
      • +: {{ orientations["+"] }}
      • -: {{ orientations["-"] }}
    • {% endfor %}
  • {% endfor %}
{% endif %} {% if config.RSS_LENGTH is defined %}

RSS Heptamer and nonamer lengths

    {% for length, value in config.RSS_LENGTH.items() %}
  • {{ length }}: {{ value }}
  • {% endfor %}
{% endif %} {% if config.RSS_MERS is defined %}

RSS Heptamer and nonamer

    {% for length, mers in config.RSS_MERS.items() %}
  • {{ length }}
      {% for mer in mers %}
    • {{ mer }}
    • {% endfor %}
  • {% endfor %}
{% endif %}
{% if qc_data%}

Quality control data

{% for folder in qc_data.keys() %} {% endfor %}
{% for folder, files in qc_data.items() %}
{% for row in files %} {% endfor %}
File Format Type Num Seqs Sum Len Min Len Avg Len Max Len
{{ row.file }} {{ row.format }} {{ row.type }} {{ row.num_seqs }} {{ row.sum_len }} {{ row.min_len }} {{ row.avg_len }} {{ row.max_len }}
{% endfor %}
{% endif %} {% if quast_data %}

Assembly data (QUAST)

{% for folder in quast_data.keys() %} {% endfor %}
{% for folder, data in quast_data.items() %}
{% for column in data.transposed_report[0].keys() %} {% endfor %} {% for row in data.transposed_report %} {% for value in row.values() %} {% endfor %} {% endfor %}
{{ column }}
{{ value }}

Assembly PDFs

{% for pdf in data.pdfs %}
{% endfor %}
{% endfor %}
{% endif %} {% if busco_data %}

BUSCO Data

{% for chromosome in busco_data.keys() %} {% endfor %}
{% for chromosome, haplotypes in busco_data.items() %}
{% for haplotype, metrics in haplotypes.items() %} {% endfor %}
Haplotype Single BUSCOs Fragmented BUSCOs Duplicates BUSCOs Missing BUSCOs
{{ haplotype|capitalize }} {{ metrics['Single BUSCOs'] }} {{ metrics['Fragmented BUSCOs'] }} {{ metrics['Duplicates BUSCOs'] }} {{ metrics['Missing BUSCOs'] }}
{% endfor %}
{% endif %} {% if region_data %}

Extracted regions

{% for row in region_data %} {% endfor %}
Sample Name Region Name Haplotype Length (bps)
{{ row.sample_name }} {{ row.region_name }} {{ row.haplotype }} {{ row.length }}
{% endif %} {% if rss_meme_data %}

RSS MEME sequence motifs

{% for branch in rss_meme_data.keys() %} {% endfor %}
{% for branch, types in rss_meme_data.items() %}
{% for type in types.keys() %} {% endfor %}
{% for type, logos in types.items() %}
{% for logo in logos %}

{{ logo.folder | replace('_', ' ') }}

{{ logo.folder }} logo
{% endfor %}
{% endfor %}
{% endfor %}
{% endif %}

Annotation Summary

{% if annotation_summary_100_plus %}

Identified known segments

{% for region in annotation_summary_100_plus|groupby('Region') %} {% endfor %}
{% for region, rows in annotation_summary_100_plus|groupby('Region') %}
{% for row in rows %} {% endfor %}
Region Haplotype Function Segment Amount
{{ row.Region }} {{ row.Haplotype }} {{ row.Function }} {{ row.Segment }} {{ row.Count }}
{% endfor %} {% endif %} {% if annotation_summary_plus %}

Identified novel segments

{% for region in annotation_summary_plus|groupby('Region') %} {% endfor %}
{% for region, rows in annotation_summary_plus|groupby('Region') %}
{% for row in rows %} {% endfor %}
Region Haplotype Function Segment Amount
{{ row.Region }} {{ row.Haplotype }} {{ row.Function }} {{ row.Segment }} {{ row.Count }}
{% endfor %} {% endif %}