diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
index 463ec99d..188894a2 100644
--- a/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -2,26 +2,25 @@
 // Run SAMtools stats, flagstat and idxstats
 //
 
-params.options = [:]
-
-include { SAMTOOLS_STATS    } from '../../../modules/samtools/stats/main'    addParams( options: params.options )
-include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main' addParams( options: params.options )
-include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main' addParams( options: params.options )
+include { SAMTOOLS_STATS    } from '../../../modules/samtools/stats/main'
+include { SAMTOOLS_IDXSTATS } from '../../../modules/samtools/idxstats/main'
+include { SAMTOOLS_FLAGSTAT } from '../../../modules/samtools/flagstat/main'
 
 workflow BAM_STATS_SAMTOOLS {
     take:
-    ch_bam_bai // channel: [ val(meta), [ bam ], [bai/csi] ]
+    bam_bai // channel: [ val(meta), [ bam/cram ], [bai/csi] ]
+    fasta   // channel: [ fasta ]
 
     main:
     ch_versions = Channel.empty()
 
-    SAMTOOLS_STATS ( ch_bam_bai, [] )
+    SAMTOOLS_STATS ( bam_bai, fasta )
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions.first())
 
-    SAMTOOLS_FLAGSTAT ( ch_bam_bai )
+    SAMTOOLS_FLAGSTAT ( bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions.first())
 
-    SAMTOOLS_IDXSTATS ( ch_bam_bai )
+    SAMTOOLS_IDXSTATS ( bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions.first())
 
     emit:
diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml
index 38fe8647..e87822df 100644
--- a/subworkflows/nf-core/bam_stats_samtools/meta.yml
+++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml
@@ -1,4 +1,4 @@
-name: samtools_stats
+name: bam_stats_samtools
 description: Produces comprehensive statistics from SAM/BAM/CRAM file
 keywords:
   - statistics
@@ -24,6 +24,10 @@ input:
       type: file
       description: Index for BAM/CRAM/SAM file
       pattern: "*.{bai,crai,sai}"
+  - fasta:
+      type: file
+      description: Reference genome fasta file
+      pattern: "*.{fasta,fa}"
 # TODO Update when we decide on a standard for subworkflow docs
 output:
   - meta:
@@ -35,6 +39,14 @@ output:
       type: file
       description: File containing samtools stats output
       pattern: "*.{stats}"
+  - flagstat:
+      type: file
+      description: File containing samtools flagstat output
+      pattern: "*.{flagstat}"
+  - idxstats:
+      type: file
+      description: File containing samtools idxstats output
+      pattern: "*.{idxstats}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/subworkflows/nf-core/bam_stats_samtools/nextflow.config b/subworkflows/nf-core/bam_stats_samtools/nextflow.config
deleted file mode 100644
index 2fd55747..00000000
--- a/subworkflows/nf-core/bam_stats_samtools/nextflow.config
+++ /dev/null
@@ -1 +0,0 @@
-params.options = [:]
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 4040cfdd..16156bbf 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -2355,6 +2355,10 @@ subread/featurecounts:
   - modules/subread/featurecounts/**
   - tests/modules/subread/featurecounts/**
 
+subworkflows/bam_stats_samtools:
+  - subworkflows/nf-core/bam_stats_samtools/**
+  - tests/subworkflows/nf-core/bam_stats_samtools/**
+
 svdb/merge:
   - modules/svdb/merge/**
   - tests/modules/svdb/merge/**
diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/main.nf b/tests/subworkflows/nf-core/bam_stats_samtools/main.nf
index a390c3eb..721972c6 100644
--- a/tests/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/tests/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -2,22 +2,27 @@
 
 nextflow.enable.dsl = 2
 
-include { BAM_STATS_SAMTOOLS } from '../../../../subworkflows/nf-core/bam_stats_samtools/main' addParams( options: [:] )
+include { BAM_STATS_SAMTOOLS as BAM_STATS_SAMTOOLS_SINGLE_END } from '../../../../subworkflows/nf-core/bam_stats_samtools/main'
+include { BAM_STATS_SAMTOOLS as BAM_STATS_SAMTOOLS_PAIRED_END } from '../../../../subworkflows/nf-core/bam_stats_samtools/main'
 
 workflow test_bam_stats_samtools_single_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-             file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
-             file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true)
     ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BAM_STATS_SAMTOOLS ( input )
+    BAM_STATS_SAMTOOLS_SINGLE_END ( input, fasta )
 }
 
 workflow test_bam_stats_samtools_paired_end {
-    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)
+    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)
     ]
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    BAM_STATS_SAMTOOLS ( input )
+    BAM_STATS_SAMTOOLS_PAIRED_END ( input, fasta )
 }
diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config b/tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config
new file mode 100644
index 00000000..3a1c4fc8
--- /dev/null
+++ b/tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config
@@ -0,0 +1,13 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: '.*:BAM_STATS_SAMTOOLS_SINGLE_END:.*' {
+        ext.prefix = { "${meta.id}.single_end.sorted.bam" }
+    }
+
+    withName: '.*:BAM_STATS_SAMTOOLS_PAIRED_END:.*' {
+        ext.prefix = { "${meta.id}.paired_end.sorted.bam" }
+    }
+
+}
\ No newline at end of file
diff --git a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml
index 2b2e45d1..5c029590 100644
--- a/tests/subworkflows/nf-core/bam_stats_samtools/test.yml
+++ b/tests/subworkflows/nf-core/bam_stats_samtools/test.yml
@@ -1,13 +1,14 @@
 - name: bam stats samtools single-end
-  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_single_end -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config
   tags:
     - subworkflows
-    # - subworkflows/bam_stats_samtools
+    - subworkflows/bam_stats_samtools
+    - bam_stats_samtools
     # Modules
-    # - samtools
-    # - samtools/stats
-    # - samtools/idxstats
-    # - samtools/flagstat
+    - samtools
+    - samtools/stats
+    - samtools/idxstats
+    - samtools/flagstat
   files:
     - path: ./output/samtools/test.single_end.sorted.bam.flagstat
       md5sum: 2191911d72575a2358b08b1df64ccb53
@@ -16,15 +17,16 @@
     - path: ./output/samtools/test.single_end.sorted.bam.stats
 
 - name: bam stats samtools paired-end
-  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/subworkflows/nf-core/bam_stats_samtools -entry test_bam_stats_samtools_paired_end -c ./tests/config/nextflow.config -c ./tests/subworkflows/nf-core/bam_stats_samtools/nextflow.config
   tags:
     - subworkflows
-    # - subworkflows/bam_stats_samtools
-    # # Modules
-    # - samtools
-    # - samtools/stats
-    # - samtools/idxstats
-    # - samtools/flagstat
+    - subworkflows/bam_stats_samtools
+    - bam_stats_samtools
+    # Modules
+    - samtools
+    - samtools/stats
+    - samtools/idxstats
+    - samtools/flagstat
   files:
     - path: ./output/samtools/test.paired_end.sorted.bam.flagstat
       md5sum: 4f7ffd1e6a5e85524d443209ac97d783