annotation done

README.md

@@ -39,7 +39,7 @@ First, prepare a samplesheet with your input data that looks as follows:
 
 **samplesheet.csv**:
 
-```
+```csv title="samplesheet.csv"
 sample,fastq_1,fastq_2
 mysampleA,sample_R1.fastq.gz,sample_R2.fastq.gz
 mysampleB,sample_R3.fastq.gz,sample_R4.fastq.gz

docs/usage.md

@@ -89,13 +89,13 @@ outdir: './results/'
 <...>
 ```
 optional parameters are:
-```
-chunk_size     # number of lines in each chunk generated from the original fastq file
-qin            # ASCII offset (33=Sanger, 64=old Solexa)
-alphabet       # allowed alphabet in the SEQ line of the FASTQ file
+```yaml title="optional_params.yaml"
+chunk_size: <int multiple of 4>   # number of lines in each chunk generated from the original fastq file
+qin:        <33/64>               # ASCII offset (33=Sanger, 64=old Solexa)
+alphabet:   <ACGTN>               # allowed alphabet in the SEQ line of the FASTQ file
 ```
 > [!WARNING]
-> Caution! Too big or too small chunk size numbers may significantly impact on performance
+> Caution! Too big or too small `chunk size` numbers may significantly impact on performance
 :::
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).