Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Author: apeltzer

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-- [#687](https://github.com/nf-core/eager/pull/687) - Adding Kraken2 unique kmer counting
+- [#687](https://github.com/nf-core/eager/pull/687) - Adds Kraken2 unique kmer counting report
 
 ### `Fixed`
 

docs/output.md

@@ -669,7 +669,7 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
 - `metagenomic_complexity_filter` - this contains the output from filtering of input reads to metagenomic classification of low-sequence complexity reads as performed by `bbduk`. This will include the filtered FASTQ files (`*_lowcomplexityremoved.fq.gz`) and also the run-time log (`_bbduk.stats`) for each sample. **Note:** there are no sections in the MultiQC report for this module, therefore you must check the `._bbduk.stats` files to get summary statistics of the filtering.
 - `metagenomic_classification/` - this contains the output for a given metagenomic classifier.
   - Running MALT will contain RMA6 files that can be loaded into MEGAN6 or MaltExtract for phylogenetic visualisation of read taxonomic assignments and aDNA characteristics respectively. Additional a `malt.log` file is provided which gives additional information such as run-time, memory usage and per-sample statistics of numbers of alignments with taxonomic assignment etc. This will also include gzip SAM files if requested.
-  - Running kraken will contain the Kraken output and report files, as well as a merged Taxon count table. You will also get a Kraken kmer duplication table, in a [KrakenUniq](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1568-0) fashion. This is very useful to check for breadth of coverage and detect read stacking. A small number of aligned reads (low coverage) and a kmer duplication >>1 is usually a sign of read stacking, usually synonym of a false positive hit. *Kmer duplication is defined as: number of kmers / number of unique kmers*
+  - Running kraken will contain the Kraken output and report files, as well as a merged Taxon count table. You will also get a Kraken kmer duplication table, in a [KrakenUniq](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1568-0) fashion. This is very useful to check for breadth of coverage and detect read stacking. A small number of aligned reads (low coverage) and a kmer duplication >1 is usually a sign of read stacking, usually indicative of a false positive hit (e.g. from over-amplified libraries). *Kmer duplication is defined as: number of kmers / number of unique kmers*
 - `maltextract/` - this contains a `results` directory in which contains the output from MaltExtract - typically one folder for each filter type, an error and a log file. The characteristics of each node (e.g. damage, read lengths, edit distances - each in different txt formats) can be seen in each sub-folder of the filter folders. Output can be visualised either with the [HOPS postprocessing script](https://github.com/rhuebler/HOPS) or [MEx-IPA](https://github.com/jfy133/MEx-IPA)
 - `consensus_sequence/` - this contains three FASTA files from VCF2Genome of a consensus sequence based on the reference FASTA with each sample's unique modifications. The main FASTA is a standard file with bases not passing the specified thresholds as Ns. The two other FASTAS (`_refmod.fasta.gz`) and (`_uncertainity.fasta.gz`) are IUPAC uncertainty codes (rather than Ns) and a special number-based uncertainty system used for other downstream tools, respectively.
 - `librarymerged_bams/` - these contain the final BAM files that would go into genotyping (if genotyping is turned on). This means the files will contain all libraries of a given sample (including trimmed non-UDG or half-UDG treated libraries, if BAM trimming turned on)