diff --git a/conf/copgt.config b/conf/copgt.config
index edbae1fe..4ac8ac5f 100644
--- a/conf/copgt.config
+++ b/conf/copgt.config
@@ -5,9 +5,10 @@
 */
 
 params {
-    callers       = "haplotypecaller"
-    only_call     = true
-    roi           = "${params.genomes_base}/Hsapiens/GRCh38/regions/coPGT-M/coPGT-M_v1.bed"
-    scatter_count = 8
-    filter        = true
+    callers                 = "haplotypecaller"
+    only_call               = true
+    roi                     = "${params.genomes_base}/Hsapiens/GRCh38/regions/coPGT-M/coPGT-M_v1.bed"
+    scatter_count           = 8
+    filter                  = true
+    skip_merged_cram_output = true
 }
diff --git a/conf/copgt_joint.config b/conf/copgt_joint.config
index 2037768e..fac72269 100644
--- a/conf/copgt_joint.config
+++ b/conf/copgt_joint.config
@@ -11,4 +11,5 @@ params {
     roi                         = "${params.genomes_base}/Hsapiens/GRCh38/regions/coPGT-M/coPGT-M_v1.bed"
     scatter_count               = 8
     filter                      = true
+    skip_merged_cram_output     = true
 }
diff --git a/conf/seqplorer.config b/conf/seqplorer.config
index b0e39b81..551b644d 100644
--- a/conf/seqplorer.config
+++ b/conf/seqplorer.config
@@ -20,4 +20,6 @@ params {
 
     vcfanno_config              = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/main/conf/Hsapiens/vcfanno/cmgg_vcfanno.toml"
     vcfanno_resources           = "${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz.tbi"
+
+    skip_merged_cram_output     = true
 }
diff --git a/conf/wes.config b/conf/wes.config
index 71105ec5..a7125fde 100644
--- a/conf/wes.config
+++ b/conf/wes.config
@@ -5,9 +5,11 @@
 */
 
 params {
-    callers             = "haplotypecaller"
-    scatter_count       = 8
-    roi                 = "${params.genomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v6.bed"
-    updio               = true
-    automap             = true
+    callers                 = "haplotypecaller"
+    scatter_count           = 8
+    roi                     = "${params.genomes_base}/Hsapiens/GRCh38/regions/CMGG_WES_analysis_ROI_v6.bed"
+    updio                   = true
+    automap                 = true
+    filter                  = true
+    skip_merged_cram_output = true
 }
diff --git a/main.nf b/main.nf
index 159727d6..b9c3e4c9 100644
--- a/main.nf
+++ b/main.nf
@@ -209,7 +209,7 @@ workflow {
     )
 
     publish:
-    merged_crams        = SMALLVARIANTS.out.merged_crams
+    crams               = SMALLVARIANTS.out.crams
     mosdepth_reports    = SMALLVARIANTS.out.mosdepth_reports
     gvcfs               = SMALLVARIANTS.out.gvcfs.filter { _meta, gvcf, _tbi -> gvcf.startsWith(workflow.workDir) } // Filtering out input GVCFs from the output publishing fixes an issue in the current implementation of the workflow output definitions: https://github.com/nextflow-io/nextflow/issues/5480
     single_beds         = SMALLVARIANTS.out.single_beds
@@ -229,7 +229,7 @@ workflow {
 }
 
 output {
-    merged_crams {
+    crams {
         path { meta, cram, crai ->
             cram >> "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.cram"
             crai >> "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.cram.crai"
diff --git a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf
index ff4bd5c3..1fe8fa9f 100644
--- a/subworkflows/local/cram_prepare_samtools_bedtools/main.nf
+++ b/subworkflows/local/cram_prepare_samtools_bedtools/main.nf
@@ -176,7 +176,6 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS {
 
     emit:
     ready_crams         = ch_ready_crams        // [ val(meta), path(cram), path(crai) ]
-    merged_crams        = ch_merged_crams       // [ val(meta), path(cram), path(crai) ]
     ready_bams          = ch_ready_bams         // [ val(meta), path(bam), path(bai) ]
     ready_beds          = ch_ready_beds         // [ val(meta), path(bed) ]
     perbase_beds        = ch_perbase_beds       // [ val(meta), path(bed), path(csi) ]
diff --git a/workflows/smallvariants.nf b/workflows/smallvariants.nf
index 99ec9b18..7c6452c1 100644
--- a/workflows/smallvariants.nf
+++ b/workflows/smallvariants.nf
@@ -416,7 +416,7 @@ workflow SMALLVARIANTS {
     ch_reports  = ch_reports.mix(CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.reports)
     def ch_single_beds = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_beds
     def ch_perbase_beds = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.perbase_beds
-    def ch_merged_crams = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.merged_crams
+    def ch_ready_crams = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.ready_crams
     def ch_mosdepth_reports = CRAM_PREPARE_SAMTOOLS_BEDTOOLS.out.mosdepth_reports
 
     //
@@ -868,7 +868,7 @@ workflow SMALLVARIANTS {
     )
 
     emit:
-    merged_crams        = ch_merged_crams               // channel: [ val(meta), path(cram), path(crai) ]
+    crams               = ch_ready_crams                // channel: [ val(meta), path(cram), path(crai) ]
     mosdepth_reports    = ch_mosdepth_reports           // channel: [ val(meta), path(mosdepth_report) ]
     gvcfs               = ch_gvcfs_ready                // channel: [ val(meta), path(gvcf), path(tbi) ]
     genomicsdb          = ch_final_genomicsdb           // channel: [ val(meta), path(genomicsdb) ]