diff --git a/main.nf b/main.nf
index 4ff48dd..e8eae7d 100644
--- a/main.nf
+++ b/main.nf
@@ -77,23 +77,41 @@ workflow WF_WISPS {
             params.colabfold_batch_size,
             params.interaction_neighbours,
             params.pool,
-            params.pool_size,
-            params.iptm_threshold
+            params.pool_size
         )
         ch_versions = ch_versions.mix(WISPS.out.versions)
 
     emit:
-    colabfold_predictions = WISPS.out.colabfold_predictions
-    boltz_predictions = WISPS.out.boltz_predictions
-    af3_predictions = WISPS.out.af3_predictions
     multiqc_report = WISPS.out.multiqc_report
     versions   = WISPS.out.versions
     collated_versions = WISPS.out.collated_versions
     ipsae_report = WISPS.out.ipsae_report
-    msa_a3m  = WISPS.out.msa_a3m
-    msa_json = WISPS.out.msa_json
-    msa_yaml = WISPS.out.msa_yaml
-    msa_csv  = WISPS.out.msa_csv
+    msa_a3m  = WISPS.out.msa_a3m.map{['a3m': it[1]]}
+    msa_json = WISPS.out.msa_json.map{['json': it[1]]}
+    msa_yaml = WISPS.out.msa_yaml.map{['yaml': it[1]]}
+    msa_csv  = WISPS.out.msa_csv.map{['csv': it[1]]}
+    colabfold_predictions = WISPS.out.colabfold_scores
+                                .join(WISPS.out.colabfold_pdb)
+                                .map { ['score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).iptm : null,
+                                        'pdb': it[2],
+                                        'confidence': it[1]] }
+                                .filter{params.iptm_threshold == 0 || it.score >= params.iptm_threshold}
+
+    boltz_predictions = WISPS.out.boltz_pae
+                            .join(WISPS.out.boltz_cif)
+                            .join(WISPS.out.boltz_confidence)
+                            .map { ['confidence': it[3], 
+                                    'cif': it[2], 
+                                    'pae': it[1], 
+                                    'score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[3].text).iptm : null] }
+                            .filter{params.iptm_threshold == 0 || it.score >= params.iptm_threshold}
+
+    af3_predictions = WISPS.out.alphafold3_confidence
+                        .join(WISPS.out.alphafold3_cif)
+                        .map { ['confidence': it[1], 
+                              'cif': it[2], 
+                              'score': params.iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).iptm : null] }
+                        .filter{params.iptm_threshold == 0 || it.score >= params.iptm_threshold}
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -139,10 +157,11 @@ workflow {
     multiqc_report = WF_WISPS.out.multiqc_report // channel: /path/to/multiqc_report.html
     //collated_versions = WF_WISPS.out.collated_versions
     ipsae_report = WF_WISPS.out.ipsae_report
-    msa_a3m  = WF_WISPS.out.msa_a3m.map{it[1]}
+    msa_a3m  = WF_WISPS.out.msa_a3m.ifEmpty([])
     msa_json = WF_WISPS.out.msa_json.ifEmpty([])
     msa_yaml = WF_WISPS.out.msa_yaml.ifEmpty([])
     msa_csv  = WF_WISPS.out.msa_csv.ifEmpty([])
+    
 }
 
 output {
@@ -175,16 +194,20 @@ output {
         path "ipsae/"
     }
     msa_a3m  {
-        path "mmseqs/"
+        path "mmseqs/a3m/"
+        enabled params.save_mmseqs_out
     }
     msa_json  {
-        path "mmseqs/"
+        path "mmseqs/json/"
+        enabled params.save_mmseqs_out
     }
     msa_yaml {
-        path 'mmseqs/'
+        path "mmseqs/yaml/"
+        enabled params.save_mmseqs_out
     }
-    msa_csv   {
-        path 'mmseqs/'
+    msa_csv  {
+        path "mmseqs/csv/"
+        enabled params.save_mmseqs_out
     }
 
 }
diff --git a/nextflow.config b/nextflow.config
index c717e89..59256c0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,8 +22,8 @@ params {
     colabfold_num_recycles     = 3
     tools                      = "boltz,colabfold"
     db                         = null
-    iptm_threshold             = 0.6
-
+    iptm_threshold             = 0
+    save_mmseqs_out            = true
     ipsae_pae_cutoff = 10
     ipsae_dist_cutoff = 10
 
@@ -78,7 +78,7 @@ params {
 }
 
 outputDir = params.outdir
-
+workflow.output.mode = params.publish_dir_mode
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4eafbfa..7237a78 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -94,6 +94,12 @@
                     "description": "Use spire DB for search",
                     "fa_icon": "fas fa-folder-open"
                 },
+                "save_mmseqs_out": {
+                    "type": "boolean",
+                    "default": true,
+                    "description": "Save the output of mmseqs in the output directory. (disable if you want to reduce storage foot print)",
+                    "fa_icon": "fas fa-microchip"
+                },
                 "email": {
                     "type": "string",
                     "description": "Email address for completion summary.",
diff --git a/workflows/wisps.nf b/workflows/wisps.nf
index 0518647..5ae2771 100644
--- a/workflows/wisps.nf
+++ b/workflows/wisps.nf
@@ -79,8 +79,7 @@ workflow WISPS {
     interaction_neighbours
     pool
     pool_size
-    iptm_threshold
-
+    
     main:
     ch_multiqc_files = Channel.empty()
     ch_confidence_scores = Channel.empty()
@@ -783,28 +782,13 @@ workflow WISPS {
     msa_json = MMSEQS_COLABFOLDSEARCH.out.json
     msa_yaml = MMSEQS_COLABFOLDSEARCH.out.yaml
     msa_csv  = MMSEQS_COLABFOLDSEARCH.out.msa_csv
-
-    colabfold_predictions = ch_colabfold_scores
-                                .join(ch_colabfold_pdb)
-                                .map { ['score': iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).iptm : null,
-                                        'pdb': it[2],
-                                        'confidence': it[1]] }
-                                .filter{iptm_threshold == 0 || it.score >= iptm_threshold}
-
-    boltz_predictions = ch_boltz_pae
-                            .join(ch_boltz_cif)
-                            .join(ch_boltz_confidence)
-                            .map { ['confidence': it[3], 
-                                    'cif': it[2], 
-                                    'pae': it[1], 
-                                    'score': iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[3].text).iptm : null] }
-                            .filter{iptm_threshold == 0 || it.score >= iptm_threshold}
-
-    af3_predictions = ch_alphafold3_confidence
-                        .join(ch_alphafold3_cif)
-                        .map { ['confidence': it[1], 
-                              'cif': it[2], 
-                              'score': iptm_threshold > 0 ? new groovy.json.JsonSlurper().parseText(it[1].text).iptm : null] }
-                        .filter{iptm_threshold == 0 || it.score >= iptm_threshold}
+    colabfold_scores = ch_colabfold_scores
+    colabfold_pdb = ch_colabfold_pdb
+    boltz_pae = ch_boltz_pae
+    boltz_cif = ch_boltz_cif
+    boltz_confidence = ch_boltz_confidence
+    alphafold3_confidence = ch_alphafold3_confidence
+    alphafold3_cif = ch_alphafold3_cif
+    
 }