updating linting failures

Author: number-25

.nf-core.yml

@@ -37,8 +37,8 @@ lint:
   multiqc_config:
     - report_comment
   nextflow_config: false
-#    - manifest.name
-#    - manifest.homePage
+  #    - manifest.name
+  #    - manifest.homePage
   nf_test_content: False
 nf_core_version: 3.3.2
 repository_type: pipeline

docs/usage.md

@@ -4,14 +4,14 @@
 
 ## Introduction
 
-
 ## Samplesheet input
 
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. It is best to specify this input parameter in `nextflow.config` or your own custom config file.
 
 ```bash
 --input '[path to samplesheet file]'
 ```
+
 ### Full samplesheet
 
 The pipeline will auto-detect whether the sequencing summary files, and reads are in the paths listed on the samplesheet. Each row represents a fastq file. Replicate refers to a technical replicate, biological replicates should be named uniquely. Be sure to pay attention to sample naming, in