[automated] Fix code linting

README.md

@@ -23,7 +23,6 @@
 
 **nf-core/taxprofiler** is a bioinformatics best-practice analysis pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It allows for in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, and produces standardised output tables for facilitating results comparison between different tools and databases.
 
-
 ## Pipeline summary
 
 ![](docs/images/taxprofiler_tube.png)

docs/output.md

@@ -157,7 +157,7 @@ The resulting `.fastq` files may _not_ always be the 'final' reads that go into
 
 In most cases you will just want to look at the PNG files which contain the extrapolation information for estimating how much of the metagenome 'coverage' you will recover if you sequence more (i.e., to help indicate at what point you will just keep sequencing redundant reads that provide no more new taxonomic information).
 
-  The `.npo` files can be used for re-generating and customising the plots using the companion `Nonpareil` R package.
+The `.npo` files can be used for re-generating and customising the plots using the companion `Nonpareil` R package.
 
 ### Porechop
 

docs/usage.md

@@ -275,22 +275,21 @@ Before using this tool please note the following caveats:
 :::warning
 
 - It is not recommended to keep unmerged (`--shortread_qc_includeunmerged`) reads when using the calculation.
-- Your shortest reads _after_ processing should not go below 24bp 
-
-    If the 'kmer' value is not correct, make sure your shortest reads _after_ processing is not less than 24bp.
-
-    If this is the case you will need to specify in a custom config
-
-    ```nextflow
-    process {
-      withName: NONPAREIL_NONPAREIL {
-        ext.args = { "-k <NUMBER>" }
-        }
-    }
-    ```
-
-    Where `<NUMBER>` should be at least the shortest read in your library
-:::
+- Your shortest reads _after_ processing should not go below 24bp
+      If the 'kmer' value is not correct, make sure your shortest reads _after_ processing is not less than 24bp.
+
+      If this is the case you will need to specify in a custom config
+
+      ```nextflow
+      process {
+        withName: NONPAREIL_NONPAREIL {
+          ext.args = { "-k <NUMBER>" }
+          }
+      }
+      ```
+
+      Where `<NUMBER>` should be at least the shortest read in your library
+  :::
 
 #### Complexity Filtering