diff --git a/modules/nf-core/chromap/chromap/main.nf b/modules/nf-core/chromap/chromap/main.nf
index f47995b3756..5b7631cb54c 100644
--- a/modules/nf-core/chromap/chromap/main.nf
+++ b/modules/nf-core/chromap/chromap/main.nf
@@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::chromap=0.2.1 bioconda::samtools=1.16.1"
+    conda "bioconda::chromap=0.2.4 bioconda::samtools=1.16.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:25259bafb105193269a9fd7595434c6fbddd4d3b-0' :
-        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:25259bafb105193269a9fd7595434c6fbddd4d3b-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0' :
+        'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:5b2e433ab8b3d1ef098fc944b567fd98caa23f56-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/chromap/index/main.nf b/modules/nf-core/chromap/index/main.nf
index 0630c614d35..25ee6a7eb63 100644
--- a/modules/nf-core/chromap/index/main.nf
+++ b/modules/nf-core/chromap/index/main.nf
@@ -2,10 +2,10 @@ process CHROMAP_INDEX {
     tag "$fasta"
     label 'process_medium'
 
-    conda "bioconda::chromap=0.2.1"
+    conda "bioconda::chromap=0.2.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' :
-        'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }"
+        'https://depot.galaxyproject.org/singularity/chromap:0.2.4--hd03093a_0' :
+        'quay.io/biocontainers/chromap:0.2.4--hd03093a_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/tests/modules/nf-core/chromap/chromap/test.yml b/tests/modules/nf-core/chromap/chromap/test.yml
index 6c507773387..7c1a9a0edcf 100644
--- a/tests/modules/nf-core/chromap/chromap/test.yml
+++ b/tests/modules/nf-core/chromap/chromap/test.yml
@@ -28,5 +28,5 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/test.bam
-      md5sum: 28ccaa8e39ecf5617dc270bdd7ddf1ba
+      md5sum: 7f8af20a3fa52b2a8967977f0376f466
     - path: output/chromap/versions.yml
diff --git a/tests/modules/nf-core/chromap/index/test.yml b/tests/modules/nf-core/chromap/index/test.yml
index d71767471d8..e3de1391482 100644
--- a/tests/modules/nf-core/chromap/index/test.yml
+++ b/tests/modules/nf-core/chromap/index/test.yml
@@ -6,4 +6,3 @@
   files:
     - path: output/chromap/genome.index
     - path: output/chromap/versions.yml
-      md5sum: fc5c80190d0622ea3e979e6862f8e32b
diff --git a/tests/subworkflows/nf-core/fastq_align_chromap/test.yml b/tests/subworkflows/nf-core/fastq_align_chromap/test.yml
index c9b49f7bb16..0e79cd7d4f7 100644
--- a/tests/subworkflows/nf-core/fastq_align_chromap/test.yml
+++ b/tests/subworkflows/nf-core/fastq_align_chromap/test.yml
@@ -51,7 +51,7 @@
     - path: ./output/samtools/test.sorted.bam.bai
       # samtools stats
     - path: ./output/samtools/test.sorted.bam.flagstat
-      md5sum: 7845b46e1dfdb6cea776bab7acf6f1e3
+      md5sum: 2fa0d90162a1b655863796c2a6bd8f45
     - path: ./output/samtools/test.sorted.bam.idxstats
       md5sum: 1adb27b52d4d64b826f48b59d61dcd4d
     - path: ./output/samtools/test.sorted.bam.stats