fix TOC

docs/output.md

@@ -27,42 +27,6 @@ The directories listed below will be created in the results directory after the
     - [Nanopore: Variants long table](#nanopore-variants-long-table)
   - [Nanopore: Workflow reporting](#nanopore-workflow-reporting)
     - [Nanopore: MultiQC](#nanopore-multiqc)
-- [Illumina: Pipeline overview](#illumina-pipeline-overview)
-  - [Illumina: Preprocessing](#illumina-preprocessing)
-    - [cat](#cat)
-    - [FastQC](#fastqc)
-    - [fastp](#fastp)
-    - [Kraken 2](#kraken-2)
-  - [Illumina: Variant calling](#illumina-variant-calling)
-    - [Bowtie 2](#bowtie-2)
-    - [SAMtools](#samtools)
-    - [iVar trim](#ivar-trim)
-    - [picard MarkDuplicates](#picard-markduplicates)
-    - [picard CollectMultipleMetrics](#picard-collectmultiplemetrics)
-    - [mosdepth](#mosdepth)
-    - [iVar variants](#ivar-variants)
-    - [BCFTools call](#bcftools-call)
-    - [SnpEff and SnpSift](#snpeff-and-snpsift)
-    - [Freyja](#freyja)
-    - [ASCIIGenome](#asciigenome)
-    - [iVar consensus](#ivar-consensus)
-    - [BCFTools and BEDTools](#bcftools-and-bedtools)
-    - [QUAST](#quast)
-    - [Pangolin](#pangolin)
-    - [Nextclade](#nextclade)
-    - [Variants long table](#variants-long-table)
-  - [Illumina: De novo assembly](#illumina-de-novo-assembly)
-    - [Cutadapt](#cutadapt)
-    - [SPAdes](#spades)
-    - [Unicycler](#unicycler)
-    - [minia](#minia)
-    - [BLAST](#blast)
-    - [ABACAS](#abacas)
-    - [PlasmidID](#plasmidid)
-    - [Assembly QUAST](#assembly-quast)
-  - [Illumina: Workflow reporting and genomes](#illumina-workflow-reporting-and-genomes)
-    - [MultiQC](#multiqc)
-    - [Reference genome files](#reference-genome-files)
 - [Pipeline information](#pipeline-information)
 
 ## Nanopore: Preprocessing
@@ -394,26 +358,6 @@ An example MultiQC report generated from a full-sized dataset can be viewed on t
 # Illumina: Pipeline overview
 
 - [Introduction](#introduction)
-- [Nanopore: Pipeline overview](#nanopore-pipeline-overview)
-  - [Nanopore: Preprocessing](#nanopore-preprocessing)
-    - [Nanopore: pycoQC](#nanopore-pycoqc)
-    - [Nanopore: artic guppyplex](#nanopore-artic-guppyplex)
-    - [Nanopore: NanoPlot](#nanopore-nanoplot)
-  - [Nanopore: Variant calling](#nanopore-variant-calling)
-    - [Nanopore: artic minion](#nanopore-artic-minion)
-  - [Nanopore: Downstream analysis](#nanopore-downstream-analysis)
-    - [Nanopore: SAMtools](#nanopore-samtools)
-    - [Nanopore: mosdepth](#nanopore-mosdepth)
-    - [Nanopore: BCFTools](#nanopore-bcftools)
-    - [Nanopore: SnpEff and SnpSift](#nanopore-snpeff-and-snpsift)
-    - [Nanopore: QUAST](#nanopore-quast)
-    - [Nanopore: Pangolin](#nanopore-pangolin)
-    - [Nanopore: Nextclade](#nanopore-nextclade)
-    - [Nanopore: Freyja](#nanopore-freyja)
-    - [Nanopore: ASCIIGenome](#nanopore-asciigenome)
-    - [Nanopore: Variants long table](#nanopore-variants-long-table)
-  - [Nanopore: Workflow reporting](#nanopore-workflow-reporting)
-    - [Nanopore: MultiQC](#nanopore-multiqc)
 - [Illumina: Pipeline overview](#illumina-pipeline-overview)
   - [Illumina: Preprocessing](#illumina-preprocessing)
     - [cat](#cat)