diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf
index 3da1d6fe..4cf98d3f 100644
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_AMPLICONCLIP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.13" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -38,7 +38,6 @@ process SAMTOOLS_AMPLICONCLIP {
     samtools \\
         ampliconclip \\
         $options.args \\
-        -@ $task.cpus \\
         $rejects \\
         $stats \\
         -b $bed \\
diff --git a/modules/samtools/faidx/main.nf b/modules/samtools/faidx/main.nf
index 80cedeab..80708084 100644
--- a/modules/samtools/faidx/main.nf
+++ b/modules/samtools/faidx/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
diff --git a/modules/samtools/fastq/main.nf b/modules/samtools/fastq/main.nf
index 0b454360..fb7e3904 100644
--- a/modules/samtools/fastq/main.nf
+++ b/modules/samtools/fastq/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_FASTQ {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -23,7 +23,7 @@ process SAMTOOLS_FASTQ {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path  "versions.yml"          , emit: versions
+    path  "versions.yml"               , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
@@ -32,7 +32,7 @@ process SAMTOOLS_FASTQ {
     """
     samtools fastq \\
         $options.args \\
-        -@ $task.cpus \\
+        --threads ${task.cpus-1} \\
         $endedness \\
         $bam
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/samtools/fixmate/main.nf b/modules/samtools/fixmate/main.nf
index e1a766a1..af1cf829 100644
--- a/modules/samtools/fixmate/main.nf
+++ b/modules/samtools/fixmate/main.nf
@@ -33,7 +33,7 @@ process SAMTOOLS_FIXMATE {
     samtools \\
         fixmate  \\
         $options.args \\
-        -@ $task.cpus \\
+        --threads ${task.cpus-1} \\
         $bam \\
         ${prefix}.bam \\
 
diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf
index f9115c6b..072a135f 100644
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_FLAGSTAT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -27,7 +27,7 @@ process SAMTOOLS_FLAGSTAT {
 
     script:
     """
-    samtools flagstat $bam > ${bam}.flagstat
+    samtools flagstat --threads ${task.cpus-1} $bam > ${bam}.flagstat
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf
index b005088a..fa0e7dc3 100644
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_IDXSTATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
diff --git a/modules/samtools/index/main.nf b/modules/samtools/index/main.nf
index 62254bc8..d66e4513 100644
--- a/modules/samtools/index/main.nf
+++ b/modules/samtools/index/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -29,7 +29,8 @@ process SAMTOOLS_INDEX {
 
     script:
     """
-    samtools index $options.args $input
+    samtools index -@ ${task.cpus-1} $options.args $input
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/merge/main.nf b/modules/samtools/merge/main.nf
index fefb423b..ab641bb9 100644
--- a/modules/samtools/merge/main.nf
+++ b/modules/samtools/merge/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_MERGE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -32,7 +32,8 @@ process SAMTOOLS_MERGE {
     def file_type = input_files[0].getExtension()
     def reference = fasta ? "--reference ${fasta}" : ""
     """
-    samtools merge ${reference} ${prefix}.${file_type} $input_files
+    samtools merge --threads ${task.cpus-1} $options.args ${reference} ${prefix}.${file_type} $input_files
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/mpileup/main.nf b/modules/samtools/mpileup/main.nf
index 9e120526..081682ed 100644
--- a/modules/samtools/mpileup/main.nf
+++ b/modules/samtools/mpileup/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_MPILEUP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
diff --git a/modules/samtools/sort/main.nf b/modules/samtools/sort/main.nf
index b30f6f45..f980b472 100644
--- a/modules/samtools/sort/main.nf
+++ b/modules/samtools/sort/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_SORT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
diff --git a/modules/samtools/stats/main.nf b/modules/samtools/stats/main.nf
index aab43410..e0a2b50d 100644
--- a/modules/samtools/stats/main.nf
+++ b/modules/samtools/stats/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_STATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -29,7 +29,8 @@ process SAMTOOLS_STATS {
     script:
     def reference = fasta ? "--reference ${fasta}" : ""
     """
-    samtools stats ${reference} ${input} > ${input}.stats
+    samtools stats --threads ${task.cpus-1} ${reference} ${input} > ${input}.stats
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/modules/samtools/view/main.nf b/modules/samtools/view/main.nf
index b7a047ee..e5ff5546 100644
--- a/modules/samtools/view/main.nf
+++ b/modules/samtools/view/main.nf
@@ -11,11 +11,11 @@ process SAMTOOLS_VIEW {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? 'bioconda::samtools=1.13' : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.14" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.14--hb421002_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
+        container "quay.io/biocontainers/samtools:1.14--hb421002_0"
     }
 
     input:
@@ -23,16 +23,17 @@ process SAMTOOLS_VIEW {
     path fasta
 
     output:
-    tuple val(meta), path("*.bam") , optional: true, emit: bam
-    tuple val(meta), path("*.cram"), optional: true, emit: cram
-    path  "versions.yml"                           , emit: versions
+    tuple val(meta), path("*.bam") , emit: bam , optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    path  "versions.yml"           , emit: versions
 
     script:
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def reference = fasta ? "--reference ${fasta} -C" : ""
     def file_type = input.getExtension()
     """
-    samtools view ${reference} $options.args $input > ${prefix}.${file_type}
+    samtools view --threads ${task.cpus-1} ${reference} $options.args $input > ${prefix}.${file_type}
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
         ${getSoftwareName(task.process)}: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/tests/modules/samtools/ampliconclip/test.yml b/tests/modules/samtools/ampliconclip/test.yml
index 9e41ce5b..9e8e1f9f 100644
--- a/tests/modules/samtools/ampliconclip/test.yml
+++ b/tests/modules/samtools/ampliconclip/test.yml
@@ -7,7 +7,7 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 1c705ebe39f68f1dac164733ae99c9d2
+      md5sum: 678f9ab04fbe3206f0f96e170fd833e9
 
 - name: samtools ampliconclip no stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c tests/config/nextflow.config
@@ -16,9 +16,9 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: 86c7bfb5378d57b16855c5b399000b2a
+      md5sum: bbf65ea626539d96c8271e17d1fc988b
     - path: output/samtools/test.cliprejects.bam
-      md5sum: 8e2eea2c0005b4d4e77c0eb549599133
+      md5sum: a0bee15aead020d16d0c81bd9667df46
 
 - name: samtools ampliconclip with stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c tests/config/nextflow.config
@@ -27,8 +27,8 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: d96f5eebef0ff4635e68090e89756d4a
+      md5sum: f5a3611ecad34ba2dde77096e1c7dd93
     - path: output/samtools/test.cliprejects.bam
-      md5sum: ad83a523d6ff1c58caade4ddafbaaed7
+      md5sum: 90ee7ce908b4bdb89ab41e4410de9012
     - path: output/samtools/test.clipstats.txt
-      md5sum: 6fbde83d658cd2813b79900d33800d1d
+      md5sum: fc23355e1743d47f2541f2cb1a7a0cda
diff --git a/tests/modules/samtools/fixmate/test.yml b/tests/modules/samtools/fixmate/test.yml
index c7864c04..0b3aa2a9 100644
--- a/tests/modules/samtools/fixmate/test.yml
+++ b/tests/modules/samtools/fixmate/test.yml
@@ -1,8 +1,8 @@
 - name: samtools fixmate test_samtools_fixmate
   command: nextflow run tests/modules/samtools/fixmate -entry test_samtools_fixmate -c tests/config/nextflow.config
   tags:
-    - samtools/fixmate
     - samtools
+    - samtools/fixmate
   files:
     - path: output/samtools/test.bam
-      md5sum: 92c8463710cdcaef2010aa02ed9e01fd
+      md5sum: a4092657a4b17170c7702a76cbf192a1
diff --git a/tests/modules/samtools/index/test.yml b/tests/modules/samtools/index/test.yml
index 66ab8211..279b99d8 100644
--- a/tests/modules/samtools/index/test.yml
+++ b/tests/modules/samtools/index/test.yml
@@ -1,4 +1,4 @@
-- name: samtools index bai
+- name: samtools index test_samtools_index_bai
   command: nextflow run tests/modules/samtools/index -entry test_samtools_index_bai -c tests/config/nextflow.config
   tags:
     - samtools
@@ -7,7 +7,7 @@
     - path: output/samtools/test.paired_end.sorted.bam.bai
       md5sum: 704c10dd1326482448ca3073fdebc2f4
 
-- name: samtools index crai
+- name: samtools index test_samtools_index_crai
   command: nextflow run tests/modules/samtools/index -entry test_samtools_index_crai -c tests/config/nextflow.config
   tags:
     - samtools
@@ -16,7 +16,7 @@
     - path: output/samtools/test.paired_end.recalibrated.sorted.cram.crai
       md5sum: 537e3d8c937bcc4e34e1cf47cd71d484
 
-- name: samtools index csi
+- name: samtools index test_samtools_index_csi
   command: nextflow run tests/modules/samtools/index -entry test_samtools_index_csi -c tests/config/nextflow.config
   tags:
     - samtools
diff --git a/tests/modules/samtools/merge/test.yml b/tests/modules/samtools/merge/test.yml
index b39ca2ec..f04aa74b 100644
--- a/tests/modules/samtools/merge/test.yml
+++ b/tests/modules/samtools/merge/test.yml
@@ -1,15 +1,15 @@
 - name: samtools merge test_samtools_merge
   command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
   tags:
-    - samtools/merge
     - samtools
+    - samtools/merge
   files:
     - path: output/samtools/test_merged.bam
 
 - name: samtools merge test_samtools_merge_cram
   command: nextflow run tests/modules/samtools/merge -entry test_samtools_merge_cram -c tests/config/nextflow.config
   tags:
-    - samtools/merge
     - samtools
+    - samtools/merge
   files:
     - path: output/samtools/test_merged.cram
diff --git a/tests/modules/samtools/sort/test.yml b/tests/modules/samtools/sort/test.yml
index 12e6669f..785ec03b 100644
--- a/tests/modules/samtools/sort/test.yml
+++ b/tests/modules/samtools/sort/test.yml
@@ -5,4 +5,4 @@
     - samtools/sort
   files:
     - path: output/samtools/test.sorted.bam
-      md5sum: bbb2db225f140e69a4ac577f74ccc90f
+      md5sum: 4adc495469724a375d5e1a9f3485e38d
diff --git a/tests/modules/samtools/stats/main.nf b/tests/modules/samtools/stats/main.nf
index 8e8b0c88..4e92b366 100644
--- a/tests/modules/samtools/stats/main.nf
+++ b/tests/modules/samtools/stats/main.nf
@@ -14,9 +14,9 @@ workflow test_samtools_stats {
 }
 
 workflow test_samtools_stats_cram {
-   input = [ [ id: 'test' ], // meta map
-               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
-               file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
+   input = [ [ id: 'test', single_end:true ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
             ]
     fasta   = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
 
diff --git a/tests/modules/samtools/stats/test.yml b/tests/modules/samtools/stats/test.yml
index a194c666..c186665a 100644
--- a/tests/modules/samtools/stats/test.yml
+++ b/tests/modules/samtools/stats/test.yml
@@ -1,17 +1,17 @@
 - name: samtools stats test_samtools_stats
   command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
   tags:
-    - samtools
     - samtools/stats
+    - samtools
   files:
     - path: output/samtools/test.paired_end.sorted.bam.stats
-      md5sum: a7f36cf11fd3bf97e0a0ae29c0627296
+      md5sum: 09146eeecfcae2a84fb8615c86cd8d64
 
 - name: samtools stats test_samtools_stats_cram
   command: nextflow run tests/modules/samtools/stats -entry test_samtools_stats_cram -c tests/config/nextflow.config
   tags:
-    - samtools
     - samtools/stats
+    - samtools
   files:
     - path: output/samtools/test.paired_end.recalibrated.sorted.cram.stats
-      md5sum: bd55a1da30028403f4b66dacf7a2a20e
+      md5sum: 62377b29c3f6253e37308a28d13a496d
diff --git a/tests/subworkflows/nf-core/align_bowtie2/test.yml b/tests/subworkflows/nf-core/align_bowtie2/test.yml
index 116ea961..07c0b1b4 100644
--- a/tests/subworkflows/nf-core/align_bowtie2/test.yml
+++ b/tests/subworkflows/nf-core/align_bowtie2/test.yml
@@ -37,7 +37,7 @@
     - path: ./output/samtools/test.sorted.bam.idxstats
       md5sum: e16eb632f7f462514b0873c7ac8ac905
     - path: ./output/samtools/test.sorted.bam.stats
-      md5sum: 2d837cd72432cd856fca70d33f02ffb5
+      md5sum: d9eb909c2cde69d6ae83999a72d770d7
 
 - name: align bowtie2 paired-end
   command: nextflow run ./tests/subworkflows/nf-core/align_bowtie2 -entry test_align_bowtie2_paired_end -c tests/config/nextflow.config
@@ -78,4 +78,4 @@
     - path: ./output/samtools/test.sorted.bam.idxstats
       md5sum: 29ff2fa56d35b2a47625b8f517f1a947
     - path: ./output/samtools/test.sorted.bam.stats
-      md5sum: 98aa88a39d26244c89bd4e577953fb48
+      md5sum: d0c7a1a4fbd2c1aed437ca419a9e344f
diff --git a/tests/subworkflows/nf-core/bam_sort_samtools/test.yml b/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
index 88ea9d5a..b84735e5 100644
--- a/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
+++ b/tests/subworkflows/nf-core/bam_sort_samtools/test.yml
@@ -4,15 +4,15 @@
     - subworkflows/bam_sort_samtools
     - subworkflows/bam_stats_samtools
     # Modules
-    # - samtools
-    # - samtools/index
-    # - samtools/sort
-    # - samtools/stats
-    # - samtools/idxstats
-    # - samtools/flagstat
+    - samtools
+    - samtools/index
+    - samtools/sort
+    - samtools/stats
+    - samtools/idxstats
+    - samtools/flagstat
   files:
     - path: ./output/samtools/test.sorted.bam
-      md5sum: e4c77897d6824ce4df486d1b100618af
+      md5sum: 8b56bb7d26ced04112f712250d915aaa
     - path: ./output/samtools/test.sorted.bam.bai
       md5sum: a70940ce9ba2e700ec2984e0a6526099
       # samtools stats
@@ -36,7 +36,7 @@
     # - samtools/flagstat
   files:
     - path: ./output/samtools/test.sorted.bam
-      md5sum: bbb2db225f140e69a4ac577f74ccc90f
+      md5sum: 4adc495469724a375d5e1a9f3485e38d
     - path: ./output/samtools/test.sorted.bam.bai
       md5sum: 20c91e3a0fd4661d7cb967f40d2486ba
       # samtools stats