diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0d2fca8bba3..c4679880018 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -214,6 +214,10 @@ jobs:
             tags: parabricks/applybqsr
           - profile: "conda"
             tags: parabricks/fq2bam
+          - profile: "conda"
+            tags: picard/collecthsmetrics
+          - profile: "conda"
+            tags: picard/collectwgsmetrics
           - profile: "conda"
             tags: scimap/mcmicro
           - profile: "conda"
@@ -264,6 +268,8 @@ jobs:
             tags: subworkflows/fasta_clean_fcs
           - profile: "conda"
             tags: islandpath
+          - profile: "conda"
+            tags: subworkflows/bam_qc_picard
     env:
       NXF_ANSI_LOG: false
       SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf
index a1ea994eff4..3de3f2eb06c 100644
--- a/modules/nf-core/picard/addorreplacereadgroups/main.nf
+++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf
@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf
index 1f3424debc5..1d7df1d8c9b 100644
--- a/modules/nf-core/picard/bedtointervallist/main.nf
+++ b/modules/nf-core/picard/bedtointervallist/main.nf
@@ -2,10 +2,10 @@ process PICARD_BEDTOINTERVALLIST {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bed)
diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf
index 718442613a4..9a7c27b131f 100644
--- a/modules/nf-core/picard/cleansam/main.nf
+++ b/modules/nf-core/picard/cleansam/main.nf
@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf
index d721bc6ffe2..522efc17099 100644
--- a/modules/nf-core/picard/collecthsmetrics/main.nf
+++ b/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(bait_intervals), path(target_intervals)
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
index 1d538fae38c..02ce25c3ce2 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf
+++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTINSERTSIZEMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf
index 91fe91702c4..ec3834e2cca 100644
--- a/modules/nf-core/picard/collectmultiplemetrics/main.nf
+++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bam), path(bai)
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
index 329938b9463..44ea068424d 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf
+++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTRNASEQMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf
index 1d59334c14e..34563b96a96 100644
--- a/modules/nf-core/picard/collectwgsmetrics/main.nf
+++ b/modules/nf-core/picard/collectwgsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0 r::r-base"
+    conda "bioconda::picard=3.1.0 r::r-base"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
index d07cc673620..a0a7c2b652e 100644
--- a/modules/nf-core/picard/createsequencedictionary/main.nf
+++ b/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf
index 86bd8782543..2621872c430 100644
--- a/modules/nf-core/picard/crosscheckfingerprints/main.nf
+++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf
@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)
diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf
index 0844fb747a7..e55fc2fc0d5 100644
--- a/modules/nf-core/picard/fastqtosam/main.nf
+++ b/modules/nf-core/picard/fastqtosam/main.nf
@@ -2,10 +2,10 @@ process PICARD_FASTQTOSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf
index 3712916938f..87ec71b3edf 100644
--- a/modules/nf-core/picard/filtersamreads/main.nf
+++ b/modules/nf-core/picard/filtersamreads/main.nf
@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)
diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf
index c8b61811808..310ace88ba6 100644
--- a/modules/nf-core/picard/fixmateinformation/main.nf
+++ b/modules/nf-core/picard/fixmateinformation/main.nf
@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf
index bfb004f76cf..b2b239ab1a0 100644
--- a/modules/nf-core/picard/liftovervcf/main.nf
+++ b/modules/nf-core/picard/liftovervcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
index ebfa0864d68..52c8e22af2d 100644
--- a/modules/nf-core/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf
index fc23ea0134d..093ee8aa421 100644
--- a/modules/nf-core/picard/mergesamfiles/main.nf
+++ b/modules/nf-core/picard/mergesamfiles/main.nf
@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf
index 75dd64b71dc..d90157f5950 100644
--- a/modules/nf-core/picard/renamesampleinvcf/main.nf
+++ b/modules/nf-core/picard/renamesampleinvcf/main.nf
@@ -3,10 +3,10 @@ process PICARD_RENAMESAMPLEINVCF {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml
index ac67898332d..d1486b50895 100644
--- a/modules/nf-core/picard/renamesampleinvcf/meta.yml
+++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml
@@ -3,6 +3,7 @@ description: changes name of sample in the vcf file
 keywords:
   - picard
   - picard/renamesampleinvcf
+  - vcf
 tools:
   - "picard":
       description: |
diff --git a/modules/nf-core/picard/scatterintervalsbyns/main.nf b/modules/nf-core/picard/scatterintervalsbyns/main.nf
index 4090d36eac8..25c92236986 100644
--- a/modules/nf-core/picard/scatterintervalsbyns/main.nf
+++ b/modules/nf-core/picard/scatterintervalsbyns/main.nf
@@ -2,10 +2,10 @@ process PICARD_SCATTERINTERVALSBYNS {
     tag "$fasta"
     label 'process_single'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf
index 590a79fd082..9dd0615290d 100644
--- a/modules/nf-core/picard/sortsam/main.nf
+++ b/modules/nf-core/picard/sortsam/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf
index b8b1f833cd2..6cd0b70588f 100644
--- a/modules/nf-core/picard/sortvcf/main.nf
+++ b/modules/nf-core/picard/sortvcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::picard=3.0.0"
+    conda "bioconda::picard=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' :
-        'biocontainers/picard:3.0.0--hdfd78af_1' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.1.0--hdfd78af_0' :
+        'biocontainers/picard:3.1.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/tests/modules/nf-core/picard/markduplicates/test.yml b/tests/modules/nf-core/picard/markduplicates/test.yml
index 8400ce9fd42..08bde2e764e 100644
--- a/tests/modules/nf-core/picard/markduplicates/test.yml
+++ b/tests/modules/nf-core/picard/markduplicates/test.yml
@@ -1,57 +1,38 @@
 - name: picard markduplicates test_picard_markduplicates_sorted_bam
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config
   tags:
-    - picard/markduplicates
     - picard
+    - picard/markduplicates
   files:
     - path: output/picard/test.marked.MarkDuplicates.metrics.txt
       contains:
         - "1.0	97	97"
     - path: output/picard/test.marked.bam
-      md5sum: 9963cba5c95a8d5cb632df217aa40d63
-    - path: output/picard/versions.yml
-- name: picard markduplicates test_picard_markduplicates_sorted_bam stub
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config -stub-run
-  tags:
-    - picard/markduplicates
-    - picard
-  files:
-    - path: output/picard/test.marked.MarkDuplicates.metrics.txt
-    - path: output/picard/test.marked.bam
+      md5sum: 41a9a8cbe2400fb8307ce1a7899e19b6
     - path: output/picard/versions.yml
+
 - name: picard markduplicates test_picard_markduplicates_unsorted_bam
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config
   tags:
-    - picard/markduplicates
     - picard
+    - picard/markduplicates
   files:
     - path: output/picard/test.marked.MarkDuplicates.metrics.txt
       contains:
         - "1.0	97	97"
-    - path: ./output/picard/test.marked.bam
-- name: picard markduplicates test_picard_markduplicates_unsorted_bam stub
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config -stub-run
+    - path: output/picard/test.marked.bam
+      md5sum: 6552e40d42a77bcec9f184b076e89340
+    - path: output/picard/versions.yml
+
+- name: picard markduplicates test_picard_markduplicates_sorted_cram
+  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_cram -c ./tests/config/nextflow.config
   tags:
-    - picard/markduplicates
     - picard
-  files:
-    - path: output/picard/test.marked.MarkDuplicates.metrics.txt
-    - path: ./output/picard/test.marked.bam
-- name: picard markduplicates sorted cram
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config
-  tags:
     - picard/markduplicates
-    - picard
   files:
     - path: output/picard/test.marked.MarkDuplicates.metrics.txt
       contains:
         - "1.0	0.999986	1178"
-    - path: ./output/picard/test.marked.bam
-- name: picard markduplicates sorted cram stub
-  command: nextflow run ./tests/modules/nf-core/picard/markduplicates -entry test_picard_markduplicates_sorted_cram -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/markduplicates/nextflow.config -stub-run
-  tags:
-    - picard/markduplicates
-    - picard
-  files:
-    - path: output/picard/test.marked.MarkDuplicates.metrics.txt
-    - path: ./output/picard/test.marked.bam
+    - path: output/picard/test.marked.bam
+      md5sum: 80eb6c43eb6982ee55bb06f59001cbe6
+    - path: output/picard/versions.yml
diff --git a/tests/subworkflows/nf-core/bam_markduplicates_picard/test.yml b/tests/subworkflows/nf-core/bam_markduplicates_picard/test.yml
index bd76372fcca..b83c1be3496 100644
--- a/tests/subworkflows/nf-core/bam_markduplicates_picard/test.yml
+++ b/tests/subworkflows/nf-core/bam_markduplicates_picard/test.yml
@@ -5,9 +5,9 @@
     - picard/markduplicates
     - samtools
     - samtools/index
-    - samtools/stats
-    - samtools/idxstats
     - samtools/flagstat
+    - samtools/idxstats
+    - samtools/stats
     - subworkflows
     - subworkflows/bam_markduplicates_picard
     - subworkflows/bam_stats_samtools
@@ -16,7 +16,7 @@
       contains:
         - "97"
     - path: output/picard/test.bam
-      md5sum: 922074f5709c586de8a62e6a42eb5986
+      md5sum: 75f42377c9b6ea57ef390b24877ba787
     - path: output/samtools/test.bam.bai
       md5sum: c48f2544a2c7454e3dba60f5db6eff9b
     - path: output/samtools/test.flagstat
@@ -33,9 +33,9 @@
     - picard/markduplicates
     - samtools
     - samtools/index
-    - samtools/stats
-    - samtools/idxstats
     - samtools/flagstat
+    - samtools/idxstats
+    - samtools/stats
     - subworkflows
     - subworkflows/bam_markduplicates_picard
     - subworkflows/bam_stats_samtools
@@ -44,7 +44,7 @@
       contains:
         - "0.999986"
     - path: output/picard/test.bam
-      md5sum: 48387ea956117dd39df99825b5117e28
+      md5sum: 291c3495d3ba2635acf1274e3dcfd9f5
     - path: output/samtools/test.bam.bai
       md5sum: 812ddc02ad163bab5711dbb778588a93
     - path: output/samtools/test.flagstat