Fasta_Summary - Blast

Convert blast results into standardised unified format for fasta summary generation

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/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/paired_end/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/paired_end/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/paired_end/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/paired_end/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