improve markdown linting

Author: maxibor

docs/output.md

@@ -485,8 +485,8 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
 * `sex_determination/` this contains the output for the sex determination run. This is a single `.tsv` file that includes a table with the Sample Name, the Nr of Autosomal SNPs, Nr of SNPs on the X/Y chromosome, the Nr of reads mapping to the Autosomes, the Nr of reads mapping to the X/Y chromosome, the relative coverage on the X/Y chromosomes, and the standard error associated with the relative coverages. These measures are provided for each bam file, one row per bam. If the `sexdeterrmine_bedfile` option has not been provided, the error bars cannot be trusted, and runtime will be considerably longer.
 * `nuclear_contamination/` this contains the output of the nuclear contamination processes. The directory contains one `*.X.contamination.out` file per individual, as well as `nuclear_contamination.txt` which is a summary table of the results for all individual. `nuclear_contamination.txt` contains a header, followed by one line per individual, comprised of the Method of Moments (MOM) and Maximum Likelihood (ML) contamination estimate (with their respective standard errors) for both Method1 and Method2.
 * `bedtools/` this contains two files as the output from bedtools coverage. One file contains the 'breadth' coverage (`*.breadth.gz`). This file will have the contents of your annotation file (e.g. BED/GFF), and the following subsequent columns: no. reads on feature, # bases at depth, length of feature, and % of feature. The second file (`*.depth.gz`), contains the contents of your annotation file (e.g. BED/GFF), and an additional column which is mean depth coverage (i.e. average number of reads covering each position).
-* `metagenomic_classification/` This contains the output for a given metagenomic classifer. 
-  - 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.
-  - Kraken will contain the Kraken output and report files, as well as a merged Taxon count table.
+* `metagenomic_classification/` This contains the output for a given metagenomic classifer.
+  * 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.
+  * Kraken will contain the Kraken output and report files, as well as a merged Taxon count table.
 * `MaltExtract/` this will contain 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 uncertainity system used for other downstream tools, respectively.

docs/usage.md

@@ -906,13 +906,16 @@ Turn on the metagenomic screening module.
 #### `--metagenomic_tool`
 
 Specify which taxonomic classifier to use. There are two options avaliable:
+
 - `malt` : more can be seen in the [MALT documentation](http://ab.inf.uni-tuebingen.de/data/software/malt/download/manual.pdf)
+  
 :warning: **Important** It is very important to run `nextflow clean -f` on your nextflow run directory once completed. RMA6 files are VERY large and are _copied_ from a `work/` directory into the results folder. You should clean the work directory with the command to ensure non-redundency and large HDD footprints!
-- `kraken` with [Kraken2](https://ccb.jhu.edu/software/kraken2) 
+
+- `kraken` with [Kraken2](https://ccb.jhu.edu/software/kraken2)
 
 #### `--metagenomic_min_support_reads`
 
-Specify the minimum number of reads a given taxon is required to have to be retained as a positive 'hit'. 
+Specify the minimum number of reads a given taxon is required to have to be retained as a positive 'hit'.  
 For malt, this only applies when `--malt_min_support_mode` is set to 'reads'. Default: 1 .
 
 #### `--database`
@@ -938,7 +941,6 @@ Specify what alignment algorithm to use. Options are 'Local' or 'SemiGlobal'. Lo
 
 Only when `--metagenomic_tool malt` is also supplied
 
-
 #### `--malt_top_percent`
 
 Specify the top percent value of the LCA algorthim. From the [MALT manual](http://ab.inf.uni-tuebingen.de/data/software/malt/download/manual.pdf): "For each
@@ -947,14 +949,12 @@ read, only those matches are used for taxonomic placement whose bit disjointScor
 
 Only when `--metagenomic_tool malt` is also supplied
 
-
 #### `--malt_min_support_mode`
 
 Specify whether to use a percentage, or raw number of reads as the value used to decide the minimum support a taxon requires to be retained.
 
 Only when `--metagenomic_tool malt` is also supplied
 
-
 #### `--malt_min_support_percent`
 
 Specify the minimum number of reads (as a percentage of all assigned reads) a given taxon is required to have to be retained as a positive 'hit' in the RMA6 file. This only applies when `--malt_min_support_mode` is set to 'percent'. Default 0.01.