diff --git a/rules/align.smk b/rules/align.smk
index bc8716cad..ed6799fa2 100644
--- a/rules/align.smk
+++ b/rules/align.smk
@@ -209,18 +209,6 @@ rule create_denovo_initial:
         sed -i -e "s/>.*/>${{CONSENSUS_NAME}}/" {output}
         """
 
-rule vicunaclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -rf {params.DIR}/*/*/initial_consensus
-        rm -rf {params.DIR}/*/*/references/vicuna_consensus.fasta
-        rm -rf {params.DIR}/*/*/references/initial_consensus.fasta
-        rm -rf references/initial_aln.fasta
-        rm -rf references/initial_aln_gap_removed.fasta
-        rm -rf references/MAFFT_initial_aln.*
-        """
 
 # change this to switch between VICUNA and creating a simple initial
 # initial reference
@@ -348,13 +336,6 @@ rule msa:
         rm ALL_{wildcards.kind}.fasta
         """
 
-rule msaclean:
-    shell:
-        """
-        rm -rf references/ALL_aln_*.fasta
-        rm -rf references/MAFFT_*_cohort.*
-        """
-
 
 # 4. convert alignments to REF alignment
 def get_reference_name(wildcards):
@@ -396,18 +377,6 @@ rule convert_to_ref:
         """
 
 
-rule alignclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -rf {params.DIR}/*/*/alignments
-        rm -rf {params.DIR}/*/*/QA_alignments
-        rm -rf {params.DIR}/*/*/references/ref_ambig.fasta
-        rm -rf {params.DIR}/*/*/references/ref_majority.fasta
-        rm -rf {params.DIR}/*/*/references/initial_consensus.fasta
-        """
-
 # 2-4. Alternative: align reads using bwa or bowtie
 if config.general["aligner"] == "bwa":
     rule ref_bwa_index:
@@ -571,32 +540,6 @@ elif config.general["aligner"] == "bowtie":
                 rm {params.TMP_SAM}
                 """
 
-rule bwaclean:
-    input:
-        "{}.bwt".format(reference_file)
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -f {input}
-        rm -rf {params.DIR}/*/*/alignments
-        """
-
-rule bowtieclean:
-    input:
-        INDEX1 = "{}.1.bt2".format(reference_file),
-        INDEX2 = "{}.2.bt2".format(reference_file),
-        INDEX3 = "{}.3.bt2".format(reference_file),
-        INDEX4 = "{}.4.bt2".format(reference_file),
-        INDEX5 = "{}.rev.1.bt2".format(reference_file),
-        INDEX6 = "{}.rev.2.bt2".format(reference_file)
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -f {input}
-        rm -rf {params.DIR}/*/*/alignments
-        """
 
 
 rule consensus_sequences:
diff --git a/rules/clean.smk b/rules/clean.smk
new file mode 100644
index 000000000..f5b26caa7
--- /dev/null
+++ b/rules/clean.smk
@@ -0,0 +1,112 @@
+rule extractclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -rf {params.DIR}/*/*/extracted_data
+        """
+
+
+rule trimmingclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -rf {params.DIR}/*/*/preprocessed_data
+        """
+
+
+rule vicunaclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -rf {params.DIR}/*/*/initial_consensus
+        rm -rf {params.DIR}/*/*/references/vicuna_consensus.fasta
+        rm -rf {params.DIR}/*/*/references/initial_consensus.fasta
+        rm -rf references/initial_aln.fasta
+        rm -rf references/initial_aln_gap_removed.fasta
+        rm -rf references/MAFFT_initial_aln.*
+        """
+
+
+rule msaclean:
+    shell:
+        """
+        rm -rf references/ALL_aln_*.fasta
+        rm -rf references/MAFFT_*_cohort.*
+        """
+
+
+rule alignclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -rf {params.DIR}/*/*/alignments
+        rm -rf {params.DIR}/*/*/QA_alignments
+        rm -rf {params.DIR}/*/*/references/ref_ambig.fasta
+        rm -rf {params.DIR}/*/*/references/ref_majority.fasta
+        rm -rf {params.DIR}/*/*/references/initial_consensus.fasta
+        """
+
+
+rule bwaclean:
+    input:
+        "{}.bwt".format(reference_file)
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -f {input}
+        rm -rf {params.DIR}/*/*/alignments
+        rm -rf {params.DIR}/*/*/references/ref_ambig*.fasta
+        rm -rf {params.DIR}/*/*/references/ref_majority*.fasta
+        """
+
+
+rule bowtieclean:
+    input:
+        INDEX1 = "{}.1.bt2".format(reference_file),
+        INDEX2 = "{}.2.bt2".format(reference_file),
+        INDEX3 = "{}.3.bt2".format(reference_file),
+        INDEX4 = "{}.4.bt2".format(reference_file),
+        INDEX5 = "{}.rev.1.bt2".format(reference_file),
+        INDEX6 = "{}.rev.2.bt2".format(reference_file)
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -f {input}
+        rm -rf {params.DIR}/*/*/alignments
+        rm -rf {params.DIR}/*/*/references/ref_ambig*.fasta
+        rm -rf {params.DIR}/*/*/references/ref_majority*.fasta
+        """
+
+
+rule snvclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -rf {params.DIR}/*/*/variants/SNVs
+        """
+
+
+rule savageclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm -rf {params.DIR}/*/*/variants/global/contigs_stage_?.fasta
+        rm -rf {params.DIR}/*/*/variants/global/stage_?
+        """
+
+
+rule haplocliqueclean:
+    params:
+        DIR = config.input['datadir']
+    shell:
+        """
+        rm {params.DIR}/*/*/variants/global/quasispecies.*
+        """
diff --git a/rules/haplotypes.smk b/rules/haplotypes.smk
index 37aa04e87..9354e4a6a 100644
--- a/rules/haplotypes.smk
+++ b/rules/haplotypes.smk
@@ -63,13 +63,6 @@ rule haploclique_visualization:
         {params.COMPUTE_MDS} -q {params.INPREFIX} -s {params.REGION_START} -e {params.REGION_END} {params.USE_MSA} {params.MSA} -p {output.PDF} -o {params.TSV} > {log.output} 2> >(tee {log.errfile} >&2)
         """
 
-rule haplocliqueclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm {params.DIR}/*/*/variants/global/quasispecies.*
-        """
 
 if config.input['paired']:
     rule savage:
@@ -141,12 +134,4 @@ else:
             {params.SAVAGE} -t {threads} --split {params.SPLIT} -s ${{R1}} -o {params.OUTDIR} 2> >(tee -a {log.errfile} >&2)
             """
 
-rule savageclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -rf {params.DIR}/*/*/variants/global/contigs_stage_?.fasta
-        rm -rf {params.DIR}/*/*/variants/global/stage_?
-        """
 
diff --git a/rules/quality_assurance.smk b/rules/quality_assurance.smk
index 02a5cb8e7..41a2b169d 100644
--- a/rules/quality_assurance.smk
+++ b/rules/quality_assurance.smk
@@ -69,14 +69,6 @@ rule extract:
         cat {input} | paste - - - - | sort -k1,1 -t " " | tr "\t" "\n" > {output} 2> >(tee {log.errfile} >&2)
         """
 
-rule extractclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -rf {params.DIR}/*/*/extracted_data
-        """
-
 
 # 2. clipping
 def len_cutoff(wildcards):
@@ -175,11 +167,4 @@ else:
             gzip {wildcards.dataset}/preprocessed_data/R1.fastq
             """
 
-rule trimmingclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -rf {params.DIR}/*/*/preprocessed_data
-        """
 
diff --git a/rules/snv.smk b/rules/snv.smk
index b00a52165..1fb6773e3 100644
--- a/rules/snv.smk
+++ b/rules/snv.smk
@@ -201,13 +201,6 @@ rule snv:
         fi
         """
 
-rule snvclean:
-    params:
-        DIR = config.input['datadir']
-    shell:
-        """
-        rm -rf {params.DIR}/*/*/variants/SNVs
-        """
 
 rule lofreq:
     input:
diff --git a/vpipe.snake b/vpipe.snake
index d3c248a8c..3721deae9 100644
--- a/vpipe.snake
+++ b/vpipe.snake
@@ -465,6 +465,7 @@ rule alltrimmed:
         trimmed_files
 
 
+include: "rules/clean.smk"
 include: "rules/quality_assurance.smk"
 include: "rules/align.smk"
 include: "rules/mafs.smk"