Rules

• Reference

  • Attributes

    • Desc

      • Custom - Prepare Description File

    • Comparison

    • Phylogenetic Tree

  • Download

    • Entrez - Download Sequences By Genbank Id

  • Index

    • Dict

      • Picard - Prepare Dict Index

    • Fai

      • Samtools - Prepare Fai Index

  • Phylogeny

• Assembly

  • Report

    • Quality Report

      • Fasta_Summary - Blast
      • Fasta_Summary - Coverage
      • Fasta_Summary - Mapped Reads
      • Fasta_Summary - Copy Contigs
      • Fasta_Summary - Summarize Annotations
      • Undocumented rules

    • Taxonomic Counts

      • Alpha Diversity

        • Custom - Alpha Diversity

      • Barplot

    • Assembly Graph

      • Bandage - Visualise Contig Overlaps

  • Assembler

    • Spades - Assemble Reads Into Contigs
    • Unicycler - Assemble Reads Into Contigs

• Variant

  • Report

    • Calling

      • Gatk - Fix Vcf Header
      • Tabix - Index Vcf
      • Picard - Bed To Interval List
      • Gatk - Collect Variant Calling Metrics

    • Summary

      • Custom - Summary Report

  • Caller

    • Vardict - Create Wgs Bed File
    • Vardict - Prepare Bed File
    • Vardict - Call Germline Variants
    • Vardict - Test Strand Bias
    • Vardict - Tsb To Vcf

• Mapping

  • Postprocess

    • Deduplicated

      • Picard - Mark Duplicates

    • Sorted

      • Samtools - Sort Mapped Reads

  • Mapper

    • Bowtie2 - Map Reads To Reference
    • Bwa - Map Reads To Reference
    • Bismark - Map Methyl Seq Reads To Reference

    • Indices

      • Bismark - Prepare Index
      • Bwa - Prepare Index
      • Bowtie2 - Prepare Index

  • Report

    • Quality Report

      • Qualimap - Mapping Quality Report Across Reference
      • Qualimap - Mapping Quality Report Across Panel
      • Qualimap - Summarize Quality Reports

    • Methylation

      • Bismark - Methylation Extractor
      • Bismark - Summary Report

  • Index

    • Samtools - Bam Index

• Reads

  • Report

    • Quality Report

      • Fastqc - Html Summary For Joined Reads
      • Fastqc - Html Summary For Paired Reads
      • Fastqc - Quality Report

  • Preprocess

    • Decontaminated

      • Bowtie2 - Filter Reads From Reference

    • Deduplicated

      • Fastuniq - Deduplicate Reads

    • Subsampled

      • Seqtk - Subsample Reads

    • Joined

      • Pear - Join Read Pairs
      • Pear - Concat Joined With Single

    • Trimmed

      • Trimmomatic - Trim Reads

  • Conversion

    • Pigz - Unzip File

• Classification

  • Transcripts

    • Salmon - Classify Reads
    • Salmon - Create Reference Index
    • Salmon - Prepare For Krona

  • Report

    • Taxonomic Counts

      • Barplot

        • Custom - Visualise Taxonomic Counts As Barplot

      • Count Table

        • Custom - Summarize Taxonomic Counts Into Tsv Table
        • Custom - Extract Taxonomic Level From Taxonomic Table

      • Pieplot

        • Krona - Single Sample Pieplot
        • Krona - Multi Sample Pieplot

    • Transcripts

      • Pca

        • Sklearn - Pca Comparison

      • Revigo

        • Custom - Export De Genes For Revigo

      • Count Table

        • Custom - Summarize Transcriptomic Counts Into Tsv Table

      • Html Table

        • Custom - Visualise Transcriptomic Counts In Html Table

    • Summary

      • Fasta_Summary - Blast
      • Fasta_Summary - Coverage
      • Fasta_Summary - Mapped Reads
      • Fasta_Summary - Copy Contigs
      • Fasta_Summary - Summarize Annotations
      • Undocumented rules

  • Read Based

    • Fast_Virome_Explorer - Estimate Virome Composition
    • Custom - Fill Na Values With Virusnames
    • Custom - Convert To Tpm Metric
    • Custom - Convert To Krona
    • Metaxa2 - Classify Reads
    • Metaxa2 - Create Reference Index
    • Metaxa2 - Summarize Classification
    • Metaxa2 - Prepare For Krona
    • Rdp - Classify Reads
    • Rdp - Prepare For Krona

  • Viral

    • Undocumented rules

    • Identification

      • Virfinder - Identify Viral Sequences

  • Contig Based

    • Blast - Find Homologues
    • Blast - Annotate With Taxonomy
    • Blast - Prepare Reference Index For Nucleotide
    • Blast - Prepare Reference Index For Protein

  • Differential Analysis

    • Edger - Identify Transcripts With Changed Expression

    • Filter Significant

      • Custom - Filter Significantly Expressed Transcripts