Fasta_Summary - Blast ------------------------- Convert blast results into standardised unified format for fasta summary generation **Location** - *Filepath:* /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:* /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:* /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:* /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:* /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