diff --git a/bin/bam_stats.sh b/bin/bam_stats.sh
new file mode 100755
index 0000000..e21ea06
--- /dev/null
+++ b/bin/bam_stats.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+FILE=${1}
+#LIST=$2
+
+#STAT=$(basename $(basename ${LIST}) .txt)
+echo "Filename"$'\t'"Total"$'\t'"mapped_reads"$'\t'"unmapped_reads"$'\t'"proportion_mapped"$'\t'"proportion_unmapped" > ${FILE}.mappedstats.txt
+
+
+mapped_reads=$(samtools stats ${FILE}.sorted.bam |  grep ^SN | awk 'NR == 7 {print $4}')
+unmapped_reads=$(samtools stats ${FILE}.sorted.bam |  grep ^SN | awk 'NR == 9 {print $4}')
+total=$(samtools stats ${FILE}.sorted.bam |  grep ^SN | awk 'NR == 1 {print $5}')
+proportion_mapped=$(awk "BEGIN {printf \"%.2f\n\", $mapped_reads*100/$total}")
+proportion_unmapped=$(awk "BEGIN {printf \"%.2f\n\", $unmapped_reads*100/$total}")
+printf "%s\t%s\t%s\t%s\t%s\t%s\n" $FILE $total $mapped_reads $unmapped_reads $proportion_mapped $proportion_unmapped >> ${FILE}.mappedstats.txt
+# remove bam file
+#rm -rf /MIGE/01_DATA/02_MAPPING/${FILE}*.{bam,bai} 
diff --git a/clean.nf b/clean.nf
index 395b29e..5c0dab7 100755
--- a/clean.nf
+++ b/clean.nf
@@ -184,7 +184,7 @@ include { check_own as prepare_keep } from './modules/prepare_contamination'
 
 include { clean } from './workflows/clean_wf' addParams( tool: tool, lib_pairedness: lib_pairedness )
 include { keep } from './workflows/keep_wf' addParams( tool: tool, lib_pairedness: lib_pairedness )
-
+include { summarize } from './workflows/summarize_wf'
 include { qc } from './workflows/qc_wf'
 
 /**************************
@@ -196,7 +196,15 @@ workflow {
   contamination = prepare_contamination.out
 
   clean(input_ch, contamination, nanoControlBedChannel, 'map-to-remove')
+  
+  bam_sort = clean.out.sort_bam_ch
+  
+  if (!params.bbduk) {
+   
+      summarize(bam_sort)
 
+  }
+ 
   if (params.keep){
     prepare_keep(keepFastaChannel)
     keep_fasta = prepare_keep.out
diff --git a/modules/prepare_contamination.nf b/modules/prepare_contamination.nf
index f9d8cd5..f285b8a 100644
--- a/modules/prepare_contamination.nf
+++ b/modules/prepare_contamination.nf
@@ -18,29 +18,29 @@ process download_host {
   """
   case $host in
     hsa)
-      wget 'ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz' -O host-temp.fa.gz
+      wget 'ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz' -O host-temp.fa.gz || curl 'ftp://ftp.ensembl.org/pub/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz' -o host-temp.fa.gz
       ;;
     mmu)
-      wget 'ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz' -O host-temp.fa.gz
+      wget 'ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz' -O host-temp.fa.gz || curl 'ftp://ftp.ensembl.org/pub/release-99/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz' -o host-temp.fa.gz
       ;;
     cli)
-      wget 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/935/GCF_000337935.1_Cliv_1.0/GCF_000337935.1_Cliv_1.0_genomic.fna.gz' -O host-temp.fa.gz
+      wget 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/935/GCF_000337935.1_Cliv_1.0/GCF_000337935.1_Cliv_1.0_genomic.fna.gz' -O host-temp.fa.gz || curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/337/935/GCF_000337935.1_Cliv_1.0/GCF_000337935.1_Cliv_1.0_genomic.fna.gz' -o host-temp.fa.gz
       ;;
     csa)
-      wget 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/795/GCF_000409795.2_Chlorocebus_sabeus_1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz' -O host-temp.fa.gz
+      wget 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/795/GCF_000409795.2_Chlorocebus_sabeus_1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz' -O host-temp.fa.gz || curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/409/795/GCF_000409795.2_Chlorocebus_sabeus_1.1/GCF_000409795.2_Chlorocebus_sabeus_1.1_genomic.fna.gz' -o host-temp.fa.gz
       ;;
     gga)
-      wget 'ftp://ftp.ensembl.org/pub/release-99/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.toplevel.fa.gz' -O host-temp.fa.gz
+      wget 'ftp://ftp.ensembl.org/pub/release-99/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.toplevel.fa.gz' -O host-temp.fa.gz || curl 'ftp://ftp.ensembl.org/pub/release-99/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.toplevel.fa.gz' -o host-temp.fa.gz
       ;;
     eco)
-      wget 'ftp://ftp.ensemblgenomes.org/pub/release-45/bacteria//fasta/bacteria_90_collection/escherichia_coli_k_12/dna/Escherichia_coli_k_12.ASM80076v1.dna.toplevel.fa.gz' -O host-temp.fa.gz
+      wget 'ftp://ftp.ensemblgenomes.org/pub/release-45/bacteria//fasta/bacteria_90_collection/escherichia_coli_k_12/dna/Escherichia_coli_k_12.ASM80076v1.dna.toplevel.fa.gz' -O host-temp.fa.gz || curl 'ftp://ftp.ensemblgenomes.org/pub/release-45/bacteria//fasta/bacteria_90_collection/escherichia_coli_k_12/dna/Escherichia_coli_k_12.ASM80076v1.dna.toplevel.fa.gz' -o host-temp.fa.gz
       ;;
     sc2)
-      wget 'https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3?download=true' -O host-temp.fa
+      wget 'https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3?download=true' -O host-temp.fa || curl 'https://www.ebi.ac.uk/ena/browser/api/fasta/MN908947.3?download=true' -o host-temp.fa
       gzip host-temp.fa
       ;;
     t2t)
-       wget 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz' -O host-temp.fa.gz
+       wget 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz' -O host-temp.fa.gz || curl 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/914/755/GCA_009914755.4_T2T-CHM13v2.0/GCA_009914755.4_T2T-CHM13v2.0_genomic.fna.gz' -o host-temp.fa.gz
       ;;
     *)
       echo "Unknown host ($host)."
diff --git a/modules/summarize.nf b/modules/summarize.nf
new file mode 100644
index 0000000..21793a3
--- /dev/null
+++ b/modules/summarize.nf
@@ -0,0 +1,83 @@
+process BAM_STATISTICS {
+   
+    label 'minimap2'
+    
+    publishDir (
+    
+    	path: "${params.output}/intermediate",
+	mode: params.publish_dir_mode,
+	pattern: "*.mappedstats.txt",
+	enabled: !params.no_intermediate,
+	saveAs: { fn ->
+          fn.startsWith("keep_") ? "map-to-keep/${fn.replaceAll(~'^keep_', '')}" : "map-to-remove/${fn}"
+    }
+    )
+    
+    input:
+    tuple val(name), val(type), path(bam)
+    
+
+    output:
+    path("*.mappedstats.txt")
+
+    
+    script:
+    """ 
+    bam_stats.sh ${name}
+
+    """
+    
+    stub:
+    """
+    touch ${bam.baseName}.mappedstats.txt
+    """
+}
+
+
+process COMBINE_BAM_STATISTICS {
+    
+    label 'minimap2'
+    
+    publishDir (
+    
+    	path: "${params.output}/intermediate",
+	mode: params.publish_dir_mode,
+	pattern: "combined_bam_stats.txt",
+	enabled: !params.no_intermediate,
+	saveAs: { fn ->
+          fn.startsWith("keep_") ? "map-to-keep/${fn.replaceAll(~'^keep_', '')}" : "map-to-remove/${fn}"
+    }
+    )
+    
+    tag { 'combine bam statistics files'} 
+    
+    
+    input:
+    path(bam_statistics_files)
+    
+
+    output:
+    path("combined_bam_stats.txt")
+
+    
+    script:
+    """ 
+    BAM_STATISTICS_FILES=(${bam_statistics_files})
+    
+    for index in \${!BAM_STATISTICS_FILES[@]}; do
+    BAM_STATISTICS_FILE=\${BAM_STATISTICS_FILES[\$index]}
+    
+    # add header line if first file
+    if [[ \$index -eq 0 ]]; then
+      echo "\$(head -1 \${BAM_STATISTICS_FILE})" >> combined_bam_stats.txt
+    fi
+    echo "\$(awk 'FNR==2 {print}' \${BAM_STATISTICS_FILE})" >> combined_bam_stats.txt
+    done
+
+    """
+    
+    stub:
+    """
+    touch combined_bam_stats.txt
+    """
+}
diff --git a/workflows/clean_wf.nf b/workflows/clean_wf.nf
index b61ed5b..6d6c234 100644
--- a/workflows/clean_wf.nf
+++ b/workflows/clean_wf.nf
@@ -24,7 +24,7 @@ workflow clean {
         } 
         else {
             minimap2(input, contamination) | sort_bam | index_bam | ( idxstats_from_bam & flagstats_from_bam )
-
+            
             split_bam(minimap2.out.bam)
             contamination_bam = split_bam.out.mapped
             cleaned_bam = split_bam.out.unmapped
@@ -50,6 +50,7 @@ workflow clean {
             idxstats = idxstats_from_bam.out
             flagstats = flagstats_from_bam.out
             out_reads = fastq_from_bam.out
+	    sort_bam_ch = sort_bam.out
         }
 
     emit:
@@ -58,4 +59,5 @@ workflow clean {
         flagstats
         out_reads
         bams_bai
+	sort_bam_ch
 }
diff --git a/workflows/summarize_wf.nf b/workflows/summarize_wf.nf
new file mode 100644
index 0000000..d050144
--- /dev/null
+++ b/workflows/summarize_wf.nf
@@ -0,0 +1,23 @@
+include { BAM_STATISTICS; COMBINE_BAM_STATISTICS } from '../modules/summarize'
+
+workflow summarize {
+    
+    take:
+       sorted_bam
+           
+    main:
+       BAM_STATISTICS(sorted_bam)
+       
+       collected_bam_statistics_ch = BAM_STATISTICS.out.collect( sort: {a, b -> a[0].getBaseName() <=> b[0].getBaseName()} )
+	
+	
+	COMBINE_BAM_STATISTICS(collected_bam_statistics_ch)
+	
+	// define output
+        bamstats = BAM_STATISTICS.out
+        summarystats = COMBINE_BAM_STATISTICS.out
+        
+    emit:
+        bamstats
+        summarystats
+}