diff --git a/CHANGELOG.md b/CHANGELOG.md
index c23161699..25b58f0f4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
 - [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
 - [#1547](https://github.com/nf-core/sarek/pull/1547) - Correct typo in help text in nextflow_schema.json
+- [#1556](https://github.com/nf-core/sarek/pull/1556) - Fix display of some commands in `docs/usage.md`
 
 ### Removed
 
diff --git a/docs/usage.md b/docs/usage.md
index f39e327bb..d12361f9f 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -831,9 +831,9 @@ For GATK.GRCh38 the links for each reference file and the corresponding processe
 | ascat_loci            | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip                                                         | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
 | ascat_loci_gc         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip                                                         | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
 | ascat_loci_rt         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/xlp99uneqh6nh6p/RT_G1000_hg38.zip                                                           | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
-| bwa                   | bwa-mem                                                                                                                                                                                                                                                                                                                                                                                                                                              | bwa index -p bwa/${fasta.baseName} $fasta                                                                             |                                                                                      |
-| bwamem2               | bwa-mem2                                                                                                                                                                                                                                                                                                                                                                                                                                             | bwa-mem2 index -p bwamem2/${fasta} $fasta                                                                             |                                                                                      |
-| dragmap               | DragMap                                                                                                                                                                                                                                                                                                                                                                                                                                              | dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap                                    |                                                                                      |
+| bwa                   | bwa-mem                                                                                                                                                                                                                                                                                                                                                                                                                                              | `bwa index -p bwa/${fasta.baseName} $fasta`                                                                           |                                                                                      |
+| bwamem2               | bwa-mem2                                                                                                                                                                                                                                                                                                                                                                                                                                             | `bwa-mem2 index -p bwamem2/${fasta} $fasta`                                                                           |                                                                                      |
+| dragmap               | DragMap                                                                                                                                                                                                                                                                                                                                                                                                                                              | `dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap`                                  |                                                                                      |
 | dbsnp                 | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
 | dbsnp_tbi             | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
 | dict                  | Baserecalibrator(Spark), CNNScoreVariant, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, MarkDulpicates(Spark), MergeVCFs, Mutect2, Variantrecalibrator                                                                                                                                                                                               | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |