Update output.md

Author: jfy133

docs/output.md

@@ -701,6 +701,7 @@ Each module has it's own output directory which sit alongside the `MultiQC/` dir
     * the `*.kreport` which is the old report format, without distinct minimizer count information, used by some tools such as [Pavian](https://github.com/fbreitwieser/pavian)
     * the `*.kraken2_report` which is the new kraken report format, with the distinct minimizer count information.  
     * finally, the `*.kraken.out` file are the direct output of Kraken2
+    * ⚠️ If your sample has no hits, no kraken output files will be created for that sample!
 * `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.
    `merged_bams/initial`: these contain the BAM files that would go into UDG-treatment specific BAM trimming. All libraries of the sample sample, **and** same UDG-treatment type will be in these BAM files.