diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index 7ba05ee9..08ac6eef 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
     def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
-    def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
-    def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
+    def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\
diff --git a/modules/picard/addorreplacereadgroups/main.nf b/modules/picard/addorreplacereadgroups/main.nf
index 8e1d10af..fd102f67 100644
--- a/modules/picard/addorreplacereadgroups/main.nf
+++ b/modules/picard/addorreplacereadgroups/main.nf
@@ -2,10 +2,10 @@ process PICARD_ADDORREPLACEREADGROUPS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -38,12 +38,12 @@ process PICARD_ADDORREPLACEREADGROUPS {
         -Xmx${avail_mem}g \\
         --INPUT ${bam} \\
         --OUTPUT ${prefix}.bam \\
-        -ID ${ID} \\
-        -LB ${LIBRARY} \\
-        -PL ${PLATFORM} \\
-        -PU ${BARCODE} \\
-        -SM ${SAMPLE} \\
-        -CREATE_INDEX true
+        --RGID ${ID} \\
+        --RGLB ${LIBRARY} \\
+        --RGPL ${PLATFORM} \\
+        --RGPU ${BARCODE} \\
+        --RGSM ${SAMPLE} \\
+        --CREATE_INDEX true
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/cleansam/main.nf b/modules/picard/cleansam/main.nf
index fb435911..62989565 100644
--- a/modules/picard/cleansam/main.nf
+++ b/modules/picard/cleansam/main.nf
@@ -2,10 +2,10 @@ process PICARD_CLEANSAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -31,8 +31,8 @@ process PICARD_CLEANSAM {
         -Xmx${avail_mem}g \\
         CleanSam  \\
         ${args} \\
-        -I ${bam} \\
-        -O ${prefix}.bam
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index ef7a9b9f..317aff4b 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTHSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -38,10 +38,10 @@ process PICARD_COLLECTHSMETRICS {
         CollectHsMetrics \\
         $args \\
         $reference \\
-        -BAIT_INTERVALS $bait_intervals \\
-        -TARGET_INTERVALS $target_intervals \\
-        -INPUT $bam \\
-        -OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
+        --BAIT_INTERVALS $bait_intervals \\
+        --TARGET_INTERVALS $target_intervals \\
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics
 
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index 340463a8..a653b549 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -2,10 +2,10 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -33,9 +33,9 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         -Xmx${avail_mem}g \\
         CollectMultipleMetrics \\
         $args \\
-        INPUT=$bam \\
-        OUTPUT=${prefix}.CollectMultipleMetrics \\
-        REFERENCE_SEQUENCE=$fasta
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectMultipleMetrics \\
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index f4efaa4c..e6dd49e9 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -2,13 +2,13 @@ process PICARD_COLLECTWGSMETRICS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
+    tuple val(meta), path(bam)
     path  fasta
 
     output:
@@ -32,9 +32,10 @@ process PICARD_COLLECTWGSMETRICS {
         -Xmx${avail_mem}g \\
         CollectWgsMetrics \\
         $args \\
-        INPUT=$bam \\
-        OUTPUT=${prefix}.CollectWgsMetrics.coverage_metrics \\
-        REFERENCE_SEQUENCE=$fasta
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
+        --REFERENCE_SEQUENCE $fasta
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/createsequencedictionary/main.nf b/modules/picard/createsequencedictionary/main.nf
index 96069e9f..2348c496 100644
--- a/modules/picard/createsequencedictionary/main.nf
+++ b/modules/picard/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -31,8 +31,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
         -Xmx${avail_mem}g \\
         CreateSequenceDictionary  \\
         $args \\
-        R=$fasta \\
-        O=${prefix}.dict
+        --REFERENCE $fasta \\
+        --OUTPUT ${prefix}.dict
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/crosscheckfingerprints/main.nf b/modules/picard/crosscheckfingerprints/main.nf
index b3dface5..d3b59402 100644
--- a/modules/picard/crosscheckfingerprints/main.nf
+++ b/modules/picard/crosscheckfingerprints/main.nf
@@ -2,10 +2,10 @@ process PICARD_CROSSCHECKFINGERPRINTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input1)
diff --git a/modules/picard/filtersamreads/main.nf b/modules/picard/filtersamreads/main.nf
index ab75abfa..adedcdc2 100644
--- a/modules/picard/filtersamreads/main.nf
+++ b/modules/picard/filtersamreads/main.nf
@@ -2,10 +2,10 @@ process PICARD_FILTERSAMREADS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)
diff --git a/modules/picard/fixmateinformation/main.nf b/modules/picard/fixmateinformation/main.nf
index 763f3bb4..539b1082 100644
--- a/modules/picard/fixmateinformation/main.nf
+++ b/modules/picard/fixmateinformation/main.nf
@@ -2,10 +2,10 @@ process PICARD_FIXMATEINFORMATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -31,8 +31,8 @@ process PICARD_FIXMATEINFORMATION {
     picard \\
         FixMateInformation \\
         -Xmx${avail_mem}g \\
-        -I ${bam} \\
-        -O ${prefix}.bam \\
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam \\
         --VALIDATION_STRINGENCY ${STRINGENCY}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/picard/liftovervcf/main.nf b/modules/picard/liftovervcf/main.nf
index cdbd637e..c92abfeb 100644
--- a/modules/picard/liftovervcf/main.nf
+++ b/modules/picard/liftovervcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_LIFTOVERVCF {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
@@ -35,11 +35,11 @@ process PICARD_LIFTOVERVCF {
         -Xmx${avail_mem}g \\
         LiftoverVcf \\
         $args \\
-        I=$input_vcf \\
-        O=${prefix}.lifted.vcf.gz \\
-        CHAIN=$chain \\
-        REJECT=${prefix}.unlifted.vcf.gz \\
-        R=$fasta
+        --INPUT $input_vcf \\
+        --OUTPUT ${prefix}.lifted.vcf.gz \\
+        --CHAIN $chain \\
+        --REJECT ${prefix}.unlifted.vcf.gz \\
+        --REFERENCE_SEQUENCE $fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/markduplicates/main.nf b/modules/picard/markduplicates/main.nf
index e754a587..1565c647 100644
--- a/modules/picard/markduplicates/main.nf
+++ b/modules/picard/markduplicates/main.nf
@@ -2,10 +2,10 @@ process PICARD_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
@@ -33,9 +33,9 @@ process PICARD_MARKDUPLICATES {
         -Xmx${avail_mem}g \\
         MarkDuplicates \\
         $args \\
-        I=$bam \\
-        O=${prefix}.bam \\
-        M=${prefix}.MarkDuplicates.metrics.txt
+        --INPUT $bam \\
+        --OUTPUT ${prefix}.bam \\
+        --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/mergesamfiles/main.nf b/modules/picard/mergesamfiles/main.nf
index ef5c3980..1e32c63a 100644
--- a/modules/picard/mergesamfiles/main.nf
+++ b/modules/picard/mergesamfiles/main.nf
@@ -2,10 +2,10 @@ process PICARD_MERGESAMFILES {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
@@ -33,8 +33,8 @@ process PICARD_MERGESAMFILES {
             -Xmx${avail_mem}g \\
             MergeSamFiles \\
             $args \\
-            ${'INPUT='+bam_files.join(' INPUT=')} \\
-            OUTPUT=${prefix}.bam
+            ${'--INPUT '+bam_files.join(' --INPUT ')} \\
+            --OUTPUT ${prefix}.bam
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             picard: \$( echo \$(picard MergeSamFiles --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
diff --git a/modules/picard/sortsam/main.nf b/modules/picard/sortsam/main.nf
index adec17cb..cee60fd1 100644
--- a/modules/picard/sortsam/main.nf
+++ b/modules/picard/sortsam/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTSAM {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/picard/sortvcf/main.nf b/modules/picard/sortvcf/main.nf
index 4047545e..fb8dbb79 100644
--- a/modules/picard/sortvcf/main.nf
+++ b/modules/picard/sortvcf/main.nf
@@ -2,10 +2,10 @@ process PICARD_SORTVCF {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
+    conda (params.enable_conda ? "bioconda::picard=2.27.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
-        'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:2.27.1--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.27.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
@@ -22,8 +22,8 @@ process PICARD_SORTVCF {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def seq_dict = sequence_dict ? "-SEQUENCE_DICTIONARY $sequence_dict" : ""
-    def reference = reference ? "-REFERENCE_SEQUENCE $reference" : ""
+    def seq_dict = sequence_dict ? "--SEQUENCE_DICTIONARY $sequence_dict" : ""
+    def reference = reference ? "--REFERENCE_SEQUENCE $reference" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard SortVcf] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
diff --git a/subworkflows/nf-core/bam_qc_picard/main.nf b/subworkflows/nf-core/bam_qc_picard/main.nf
new file mode 100644
index 00000000..e38697c3
--- /dev/null
+++ b/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -0,0 +1,41 @@
+//
+// Run QC steps on BAM/CRAM files using Picard
+//
+
+include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../modules/picard/collectmultiplemetrics/main'
+include { PICARD_COLLECTWGSMETRICS      } from '../../../modules/picard/collectwgsmetrics/main'
+include { PICARD_COLLECTHSMETRICS       } from '../../../modules/picard/collecthsmetrics/main'
+
+workflow BAM_QC_PICARD {
+    take:
+    ch_bam              // channel: [ val(meta), [ bam ]]
+    ch_fasta            // channel: [ fasta ]
+    ch_fasta_fai        // channel: [ fasta_fai ]
+    ch_bait_interval    // channel: [ bait_interval ]
+    ch_target_interval  // channel: [ target_interval ]
+
+    main:
+    ch_versions = Channel.empty()
+    ch_coverage_metrics = Channel.empty()
+
+    PICARD_COLLECTMULTIPLEMETRICS( ch_bam, ch_fasta )
+    ch_versions = ch_versions.mix(PICARD_COLLECTMULTIPLEMETRICS.out.versions.first())
+
+    if (ch_bait_interval || ch_target_interval) {
+        if (!ch_bait_interval) log.error("Bait interval channel is empty")
+        if (!ch_target_interval) log.error("Target interval channel is empty")
+        PICARD_COLLECTHSMETRICS( ch_bam, ch_fasta, ch_fasta_fai, ch_bait_interval, ch_target_interval )
+        ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTHSMETRICS.out.metrics)
+        ch_versions = ch_versions.mix(PICARD_COLLECTHSMETRICS.out.versions.first())
+    } else {
+        PICARD_COLLECTWGSMETRICS( ch_bam, ch_fasta )
+        ch_versions = ch_versions.mix(PICARD_COLLECTWGSMETRICS.out.versions.first())
+        ch_coverage_metrics = ch_coverage_metrics.mix(PICARD_COLLECTWGSMETRICS.out.metrics)
+    }
+
+    emit:
+    coverage_metrics    = ch_coverage_metrics                       // channel: [ val(meta), [ coverage_metrics ] ]
+    multiple_metrics    = PICARD_COLLECTMULTIPLEMETRICS.out.metrics // channel: [ val(meta), [ multiple_metrics ] ]
+
+    versions            = ch_versions                               // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-core/bam_qc_picard/meta.yml b/subworkflows/nf-core/bam_qc_picard/meta.yml
new file mode 100644
index 00000000..c45215d1
--- /dev/null
+++ b/subworkflows/nf-core/bam_qc_picard/meta.yml
@@ -0,0 +1,60 @@
+name: bam_qc
+description: Produces comprehensive statistics from BAM file
+keywords:
+  - statistics
+  - counts
+  - hs_metrics
+  - wgs_metrics
+  - bam
+  - sam
+  - cram
+modules:
+  - picard/collectmultiplemetrics
+  - picard/collectwgsmetrics
+  - picard/collecthsmetrics
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+  - fasta:
+      type: optional file
+      description: Reference fasta file
+      pattern: "*.{fasta,fa}"
+  - fasta_fai:
+      type: optional file
+      description: Reference fasta file index
+      pattern: "*.{fasta,fa}.fai"
+  - bait_intervals:
+      type: optional file
+      description: An interval list file that contains the locations of the baits used.
+      pattern: "baits.interval_list"
+  - target_intervals:
+      type: optional file
+      description: An interval list file that contains the locations of the targets.
+      pattern: "targets.interval_list"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - coverage_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics
+      pattern: "*_metrics.txt"
+  - multiple_metrics:
+      type: file
+      description: Alignment metrics files generated by picard CollectMultipleMetrics
+      pattern: "*_{metrics}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@matthdsm"
diff --git a/tests/modules/picard/addorreplacereadgroups/test.yml b/tests/modules/picard/addorreplacereadgroups/test.yml
index aa1536bb..6ee81737 100644
--- a/tests/modules/picard/addorreplacereadgroups/test.yml
+++ b/tests/modules/picard/addorreplacereadgroups/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: 7b82f3461c2d80fc6a10385e78c9427f
     - path: output/picard/versions.yml
-      md5sum: 8a2d176295e1343146ea433c79bb517f
diff --git a/tests/modules/picard/cleansam/test.yml b/tests/modules/picard/cleansam/test.yml
index 3b235d07..08dcd84d 100644
--- a/tests/modules/picard/cleansam/test.yml
+++ b/tests/modules/picard/cleansam/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: a48f8e77a1480445efc57570c3a38a68
     - path: output/picard/versions.yml
-      md5sum: e6457d7c6de51bf6f4b577eda65e57ac
diff --git a/tests/modules/picard/collectwgsmetrics/main.nf b/tests/modules/picard/collectwgsmetrics/main.nf
index 1d75a2bd..eddf5603 100644
--- a/tests/modules/picard/collectwgsmetrics/main.nf
+++ b/tests/modules/picard/collectwgsmetrics/main.nf
@@ -6,8 +6,7 @@ include { PICARD_COLLECTWGSMETRICS } from '../../../../modules/picard/collectwgs
 
 workflow test_picard_collectwgsmetrics {
     input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
diff --git a/tests/modules/picard/createsequencedictionary/test.yml b/tests/modules/picard/createsequencedictionary/test.yml
index 2a43be41..59f2dd44 100644
--- a/tests/modules/picard/createsequencedictionary/test.yml
+++ b/tests/modules/picard/createsequencedictionary/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.dict
       contains: ["SN:MT192765.1"]
     - path: output/picard/versions.yml
-      md5sum: b3d8c7ea65b8a6d3237b153d13fe2014
diff --git a/tests/modules/picard/fixmateinformation/test.yml b/tests/modules/picard/fixmateinformation/test.yml
index f12f823b..f2f9c491 100644
--- a/tests/modules/picard/fixmateinformation/test.yml
+++ b/tests/modules/picard/fixmateinformation/test.yml
@@ -7,4 +7,3 @@
     - path: output/picard/test.bam
       md5sum: 746102e8c242c0ef42e045c49d320030
     - path: output/picard/versions.yml
-      md5sum: 4329ba7cdca8f4f6018dfd5c019ba2eb
diff --git a/tests/modules/picard/liftovervcf/nextflow.config b/tests/modules/picard/liftovervcf/nextflow.config
index e1581bb9..f69fc351 100644
--- a/tests/modules/picard/liftovervcf/nextflow.config
+++ b/tests/modules/picard/liftovervcf/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    ext.args = "WARN_ON_MISSING_CONTIG=true"
+    ext.args = "--WARN_ON_MISSING_CONTIG true"
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
 }
diff --git a/tests/modules/picard/markduplicates/nextflow.config b/tests/modules/picard/markduplicates/nextflow.config
index 9178c5b1..40d46110 100644
--- a/tests/modules/picard/markduplicates/nextflow.config
+++ b/tests/modules/picard/markduplicates/nextflow.config
@@ -3,7 +3,7 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName: PICARD_MARKDUPLICATES_UNSORTED {
-        ext.args = 'ASSUME_SORT_ORDER=queryname'
+        ext.args = '--ASSUME_SORT_ORDER queryname'
     }
 
 }
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/main.nf b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
new file mode 100644
index 00000000..a3e2ed62
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_qc_picard/main.nf
@@ -0,0 +1,27 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BAM_QC_PICARD } from '../../../../subworkflows/nf-core/bam_qc_picard/main' addParams([:])
+
+workflow test_bam_qc_picard_wgs {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+    fasta   = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    BAM_QC_PICARD ( input, fasta, fasta_fai, [], [] )
+}
+
+workflow test_bam_qc_picard_targetted {
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+    fasta       = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fasta_fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    bait        = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target      = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+
+    BAM_QC_PICARD ( input, fasta, fasta_fai, bait, target )
+}
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/nextflow.config b/tests/subworkflows/nf-core/bam_qc_picard/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_qc_picard/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/subworkflows/nf-core/bam_qc_picard/test.yml b/tests/subworkflows/nf-core/bam_qc_picard/test.yml
new file mode 100644
index 00000000..7b0a6c2b
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_qc_picard/test.yml
@@ -0,0 +1,33 @@
+- name: bam qc picard wgs
+  command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_wgs -c tests/config/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/bam_qc_picard
+    # Modules
+    # - picard
+    # - picard/collectmultiplemetrics
+    # - picard/collectwgsmetrics
+  files:
+    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: ./output/picard/test.CollectWgsMetrics.coverage_metrics
+
+- name: bam qc picard targetted
+  command: nextflow run ./tests/subworkflows/nf-core/bam_qc_picard -entry test_bam_qc_picard_targetted -c tests/config/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/bam_qc_picard
+    # Modules
+    # - picard
+    # - picard/collectmultiplemetrics
+    # - picard/collecthsmetrics
+  files:
+    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+    - path: ./output/picard/test.CollectHsMetrics.coverage_metrics