diff --git a/main.nf b/main.nf
index 01dba10..eb454e6 100644
--- a/main.nf
+++ b/main.nf
@@ -227,7 +227,6 @@ workflow {
                         .map{ it -> [params.sample_id, it] }
                 )
 
-                checksum_ch = checksum_ch.mix(merge_bedfiles_BEDtools.out.bed.flatten())
                 checksum_ch = checksum_ch.mix(compress_index_BED.out.index_out.map{ it -> [it[1], it[2]]})
                 }
 
diff --git a/module/merge_bedfiles_bedtools.nf b/module/merge_bedfiles_bedtools.nf
index 5818b0f..9ff609d 100644
--- a/module/merge_bedfiles_bedtools.nf
+++ b/module/merge_bedfiles_bedtools.nf
@@ -9,9 +9,10 @@ include { generate_standard_filename } from '../external/pipeline-Nextflow-modul
 process merge_bedfiles_BEDtools {
     container params.docker_image_bedtools
 
-    publishDir path: "${params.workflow_output_dir}/output/",
+    publishDir path: "${params.workflow_output_dir}/intermediate/${task.process.replace(':','/')}",
         pattern: "*.bed",
-        mode: "copy"
+        mode: "copy",
+        enabled: params.save_intermediate_files
 
     publishDir path: "${params.log_output_dir}/process-log/",
         pattern: ".command.*",
diff --git a/nftest.yml b/nftest.yml
index 1b5f194..41c1616 100644
--- a/nftest.yml
+++ b/nftest.yml
@@ -18,9 +18,6 @@ cases:
       - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_off-target-dbSNP-depth-per-base.bed
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.off-target-dbSNP_depth-per-base.bed
         method: md5
-      - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed
-        expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed
-        method: md5
       - actual: calculate-targeted-coverage-*/TWGSAMIN000001-T002-S02-F/SAMtools-*/output/BEDtools-*_TWGSAMIN000001_TWGSAMIN000001-T002-S02-F_target-with-enriched-off-target-intervals.bed.gz
         expect: /hot/software/pipeline/pipeline-calculate-targeted-coverage/Nextflow/development/output/TWGSAMIN000001-T002-S02-F.target_with_enriched_off-target_intervals.bed.gz
         method: md5