diff --git a/conf/modules.config b/conf/modules.config
index 52bc407..fdc4e41 100755
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -51,7 +51,14 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapping-bp" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')){ null }
+                else if (filename.endsWith('.bam') || filename.endsWith('.bam.bai')){
+                    if ( params.keep_big_files == true ) { filename }
+                    else { null }
+                }
+                else { filename }
+            }
         ]
     }
     withName: SAMTOOLS_DEPTH {
@@ -59,7 +66,14 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapping-bp" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')){ null }  
+                else if ( filename.endsWith('bp-depth.tsv') ){
+                    if ( params.keep_big_files == true ) { filename }
+                    else { null }
+                }
+                else { filename }
+            }
         ]
     }
     withName: HS_FLAGSTAT {
@@ -81,17 +95,24 @@ process {
     withName: HS_FASTQ {
         ext.args = '-N'
         ext.suffix = 'hs-unmapped.'
-        ext.filt = 'hs-unmapped.'
+        ext.filt = 'hs-unmapped'
         publishDir = [
             path: { "${params.outdir}/mapping-hs" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')){ null }  
+                else if ( filename.endsWith('fastq.gz') ){
+                    if ( params.keep_big_files == true ) { filename }
+                    else { null }
+                }
+                else { filename }
+            }
         ]
     }
     withName: BP_FASTQ {
         ext.args = '-N'
         ext.suffix = 'bp-mapped.'
-        ext.filt = 'filtered.'
+        ext.filt = 'filtered'
         publishDir = [
             path: { "${params.outdir}/filteredreads" },
             mode: params.publish_dir_mode,
@@ -111,7 +132,14 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapping-hs" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')){ null }  
+                else if ( filename.endsWith('.bam') ){
+                    if ( params.keep_big_files == true ) { filename }
+                    else { null }
+                }
+                else { filename }
+            }
         ]
     }
     withName: BP_ALIGN {
@@ -119,7 +147,14 @@ process {
         publishDir = [
             path: { "${params.outdir}/mapping-bp" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')){ null }  
+                else if (filename.endsWith('.bam')){
+                    if ( params.keep_big_files == true ) { filename }
+                    else { null }
+                }
+                else { filename }
+            }
         ]
     }
     withName: BLASTN_PAIRWISE {
diff --git a/modules/nf-core/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/modules/nf-core/samtools/fastq/main.nf
index 6e55950..136374f 100644
--- a/modules/nf-core/modules/nf-core/samtools/fastq/main.nf
+++ b/modules/nf-core/modules/nf-core/samtools/fastq/main.nf
@@ -12,7 +12,7 @@ process SAMTOOLS_FASTQ {
     val(interleave)
 
     output:
-    tuple val(meta), path("*.R{1,2}.fastq.gz")     , optional:true, emit: fastq
+    tuple val(meta), path("*_R{1,2}_*.fastq.gz")   , optional:true, emit: fastq
     tuple val(meta), path("*_interleaved.fastq.gz"), optional:true, emit: interleaved
     tuple val(meta), path("*_singleton.fastq.gz")  , optional:true, emit: singleton
     tuple val(meta), path("*_other.fastq.gz")      , optional:true, emit: other
@@ -28,7 +28,7 @@ process SAMTOOLS_FASTQ {
     def filt = task.ext.filt ?: ''
     def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq.gz" :
         meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
-        "-1 ${prefix}.${filt}R1.fastq.gz -2 ${prefix}.${filt}R2.fastq.gz" // -s ${prefix}_singleton.fastq.gz"
+        "-1 ${prefix}_R1_${filt}.fastq.gz -2 ${prefix}_R2_${filt}.fastq.gz" // -s ${prefix}_singleton.fastq.gz"
     """
     samtools sort -n --threads ${task.cpus-1} $input -o ${prefix}.${suffix}namesort.bam
     samtools \\
diff --git a/nextflow.config b/nextflow.config
index 0dc5930..64bea69 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -20,6 +20,7 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
+    keep_big_files             = false  // option to keep mapping results
 
     // MultiQC options
     multiqc_config             = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 251af89..4d04e53 100755
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -41,6 +41,12 @@
                     "type": "string",
                     "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
                     "fa_icon": "fas fa-file-signature"
+                },
+                "keep_big_files": {
+                    "type": "boolean",
+                    "description": "Option to keep large intermediate *bam and *fastq files.",
+                    "default": false,
+                    "fa_icon": "fas fa-floppy-disk"
                 }
             }
         },