Fasta_Summary - Blast
-------------------------

Convert blast results into standardised unified format for fasta summary generation

**Location**

- *Filepath:* <SnakeLines_dir>/rules/classification/report/summary/fasta_summary.snake
- *Rule name:* fasta_summary__blast

**Input(s):**

- *blast:* Blast classification with taxonomy

**Output(s):**

- *tsv:* Classification in unified format

Fasta_Summary - Coverage
----------------------------

Extract mapping coverage and store it into standardised unified format for fasta summary generation

**Location**

- *Filepath:* <SnakeLines_dir>/rules/classification/report/summary/fasta_summary.snake
- *Rule name:* fasta_summary__coverage

**Input(s):**

- *qualimap:* Quality report statistics generated by Qualimap

**Output(s):**

- *tsv:* Mapping coverage in standardised unified format for fasta summary generation

Fasta_Summary - Mapped Reads
--------------------------------

Get number of mapped reads to each reference sequence and convert into standardised unified format for
fasta summary generation

**Location**

- *Filepath:* <SnakeLines_dir>/rules/classification/report/summary/fasta_summary.snake
- *Rule name:* fasta_summary__mapped_reads

**Input(s):**

- *bam:* Mapped reads in bam format
- *bai:* Index for bam file with mapped reads

**Output(s):**

- *tsv:* Mapped reads per reference sequence in standardised unified format for fasta summary generation

Fasta_Summary - Copy Contigs
--------------------------------

Separate sequences into individual fasta files and calculate basic statistics for each sequence.
Also store statistics into standardised unified format for fasta summary generation.

**Location**

- *Filepath:* <SnakeLines_dir>/rules/classification/report/summary/fasta_summary.snake
- *Rule name:* fasta_summary__copy_contigs

**Input(s):**

- *fasta:* Genomic sequences in fasta format

**Output(s):**

- *fasta:* Copy of fasta file, stored in the directory accessible from summary HTML report
- *seqinfo:* Statistics of genomic sequences in standardised unified format for fasta summary generation

Fasta_Summary - Summarize Annotations
-----------------------------------------

Generate summary HTML report with several aggregated attribute sources from various tools.

**Location**

- *Filepath:* <SnakeLines_dir>/rules/classification/report/summary/fasta_summary.snake
- *Rule name:* fasta_summary__summarize_annotations

**Input(s):**

- *template:* HTML template with basic report outline
- *fasta:* Analysed sequences in fasta format
- *attrs_seqinfo:* Basic statistics of genomic sequences - length, GC content, complexity...
- *attrs_coverage:* Mapping coverage of sequences
- *attrs_mapped_reads:* Mapped reads per genomic sequence
- *attrs_virfinder:* Probabilities of viral origin for genomic sequences - calculated by the Virfinder tool

Undocumented rules
------------------
WARNING: found  1 undocumented rules:

- rule fasta_summary__virfinder is UNDOCUMENTED
