Merge pull request #419 from nf-core/add-csv-syntax

docs/usage.md

@@ -44,7 +44,7 @@ This samplesheet is then specified on the command line as follows:
 
 The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate different runs FASTQ files of the same sample before performing profiling, when `--perform_runmerging` is supplied. Below is an example for the same sample sequenced across 3 lanes:
 
-```console
+```csv
 sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
 2612,run1,ILLUMINA,2612_run1_R1.fq.gz,,
 2612,run2,ILLUMINA,2612_run2_R1.fq.gz,,
@@ -62,7 +62,7 @@ The pipeline will auto-detect whether a sample is single- or paired-end using th
 
 A final samplesheet file consisting of both single- and paired-end data, as well as long-read FASTA files may look something like the one below. This is for 6 samples, where `2612` has been sequenced twice.
 
-```console
+```csv
 sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
 2611,ERR5766174,ILLUMINA,,,/<path>/<to>/fasta/ERX5474930_ERR5766174_1.fa.gz
 2612,ERR5766176,ILLUMINA,/<path>/<to>/fastq/ERX5474932_ERR5766176_1.fastq.gz,/<path>/<to>/fastq/ERX5474932_ERR5766176_2.fastq.gz,
@@ -110,7 +110,7 @@ An example database sheet can look as follows, where 7 tools are being used, and
 
 `kraken2` will be run twice even though only having a single 'dedicated' database because specifying `bracken` implies first running `kraken2` on the `bracken` database, as required by `bracken`.
 
-```console
+```csv
 tool,db_name,db_params,db_path
 malt,malt85,-id 85,/<path>/<to>/malt/testdb-malt/
 malt,malt95,-id 90,/<path>/<to>/malt/testdb-malt.tar.gz