diff --git a/README.md b/README.md index d306faf..317ab19 100644 --- a/README.md +++ b/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 diff --git a/docs/usage.md b/docs/usage.md index 9a481e8..bf9543c 100644 --- a/docs/usage.md +++ b/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: # number of lines in each chunk generated from the original fastq file +qin: <33/64> # ASCII offset (33=Sanger, 64=old Solexa) +alphabet: # 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).