diff --git a/subworkflows/local/pre_qc.nf b/subworkflows/local/pre_qc.nf
index ce4e2e5..e4aa683 100644
--- a/subworkflows/local/pre_qc.nf
+++ b/subworkflows/local/pre_qc.nf
@@ -14,35 +14,43 @@ workflow PRE_QC {
 
     take:
     ch_samplesheet
+    skip_ee
+    skip_merging
+    skip_dadaQC
 
     main:
     ch_versions = Channel.empty()
 
-    VSEARCH_OVERLAP(
-        ch_samplesheet
-    )
+    if (!skip_merging) {
+        VSEARCH_OVERLAP(
+            ch_samplesheet
+        )
 
-    ch_versions = ch_versions.mix(VSEARCH_OVERLAP.out.versions.first())
+        ch_versions = ch_versions.mix(VSEARCH_OVERLAP.out.versions.first())
+        MERGE_OVERLAP_CHECK(
+            VSEARCH_OVERLAP.out.merged_log.collect()
+        )
 
-    VSEARCH_EESTATS (
-        ch_samplesheet
-    )
+        OVERLAP_HEATMAP(
+            VSEARCH_OVERLAP.out.merged_stats.collect()
+        )        
+    }
 
-    ch_versions = ch_versions.mix(VSEARCH_EESTATS.out.versions.first())
+    if (!skip_ee) {
+        VSEARCH_EESTATS (
+            ch_samplesheet
+        )
 
-    MERGE_OVERLAP_CHECK(
-        VSEARCH_OVERLAP.out.merged_log.collect()
-    )
-
-    OVERLAP_HEATMAP(
-        VSEARCH_OVERLAP.out.merged_stats.collect()
-    )
-
-    PLOT_QUALITY_PROFILE (
-        ch_samplesheet
-    )
+        ch_versions = ch_versions.mix(VSEARCH_EESTATS.out.versions.first())
+    }
+    
+    if (!skip_dadaQC) {
+        PLOT_QUALITY_PROFILE (
+            ch_samplesheet
+        )
 
-    ch_versions = ch_versions.mix(PLOT_QUALITY_PROFILE.out.versions.first())
+        ch_versions = ch_versions.mix(PLOT_QUALITY_PROFILE.out.versions.first())
+    }
     
     emit:
     versions = ch_versions                     // channel: [ versions.yml ]
diff --git a/workflows/tada.nf b/workflows/tada.nf
index cee032b..60921c4 100644
--- a/workflows/tada.nf
+++ b/workflows/tada.nf
@@ -103,7 +103,10 @@ workflow TADA {
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     PRE_QC(
-        ch_samplesheet
+        ch_samplesheet,
+        params.skip_ee,
+        params.skip_merging,
+        params.skip_dadaQC
     )
 
     ch_versions = ch_versions.mix(PRE_QC.out.versions)
@@ -167,12 +170,12 @@ workflow TADA {
     // would be useful for...
     // this needs to die with an error message if method is not defined, or
     // it needs to be caught above
-    if (params.run_tree == 'phangorn') {
+    if (params.phylo_tool == 'phangorn') {
         PHANGORN(
             DECIPHER.out.alignment
         )
         ch_tree = PHANGORN.out.treeGTR
-    } else if (params.run_tree == 'fasttree') {
+    } else if (params.phylo_tool == 'fasttree') {
         FASTTREE(
             DECIPHER.out.alignment
         )
@@ -181,7 +184,7 @@ workflow TADA {
 
     ROOT_TREE(
         ch_tree,
-        params.run_tree
+        params.phylo_tool
     )
 
     // QC