nf-core · sofstam · Mar 11, 2025 · Mar 11, 2025 · Mar 11, 2025 · Mar 11, 2025
@@ -10,12 +10,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#576](https://github.com/nf-core/taxprofiler/pull/576) Sort input to krakenuniq to enable retrieval of cached batch tasks (❤️ to @muniheart for reporting and fix)
 - [#569](https://github.com/nf-core/taxprofiler/pull/569) Updated to nf-core pipeline template v3.1.2 (added by @sofstam)
 - [#571](https://github.com/nf-core/taxprofiler/pull/571) Updated to nf-core pipeline template v3.2.0 (added by @sofstam)
+-
 
 ### `Fixed`
 
 - [#580](https://github.com/nf-core/taxprofiler/pull/580) Minor documentation typo fixes (❤️ to @AlexHoratio for reporting and fix)
 - [#573](https://github.com/nf-core/taxprofiler/pull/573) Improved help messages and documentation to state many of the taxpasta related params require taxonomy files to be input (❤️ to @alexhbnr for reporting, fix by @jfy133)
 - [#578](https://github.com/nf-core/taxprofiler/pull/578) Fixed incorrect keyword in nextflow_schema.json (fix by @mashehu)
+- [#585](https://github.com/nf-core/taxprofiler/pull/585) Fixed code blocks (fix by @masheshu)
 
 ### `Dependencies`
 

@@ -59,9 +59,7 @@
 
 First, prepare a samplesheet with your input data that looks as follows:
 
-`samplesheet.csv`:
-
-```csv
+```csv title="samplesheet.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,,
@@ -72,9 +70,7 @@ Each row represents a fastq file (single-end), a pair of fastq files (paired end
 
 Additionally, you will need a database sheet that looks as follows:
 
-`databases.csv`:
-
-```csv
+```csv title="databases.csv"
 tool,db_name,db_params,db_path
 kraken2,db2,--quick,/<path>/<to>/kraken2/testdb-kraken2.tar.gz
 metaphlan,db1,,/<path>/<to>/metaphlan/metaphlan_database/