diff --git a/conf/modules_alphafold2.config b/conf/modules_alphafold2.config
index abf107b8..5ae05c26 100644
--- a/conf/modules_alphafold2.config
+++ b/conf/modules_alphafold2.config
@@ -55,16 +55,38 @@ process {
         ].join(' ').trim()
         publishDir = [
             [
-                path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}" },
+                path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
                 mode: 'copy',
-                saveAs: { filename ->
-                    if(filename.endsWith('_pae.tsv')){
+                pattern: '*.pkl',
+                enabled: params.save_base_output, 
+            ],
+            [
+                path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
+                mode: 'copy',
+                pattern: '*.json',
+                enabled: params.save_base_output, 
+            ],
+            [
+                path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
+                mode: 'copy',
+                pattern: '*.pdb',
+                enabled: params.save_base_output, 
+            ],
+            [
+                path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/base_program_output" },
+                mode: 'copy',
+                pattern: '*.{a3m,sto}',
+                enabled: params.save_base_output, 
+            ],
+            [
+                path: { "${params.outdir}/${meta.model}/${params.alphafold2_mode}/${meta.id}/proteinfold_reporting" },
+                mode: 'copy',
+                pattern: '*_{plddt,msa,ptm,iptm,pae}.tsv',
+                saveAs : { filename ->
+                  if(filename.endsWith('_pae.tsv')){
                         "paes/$filename"
-                    } else if(filename.equals('versions.yml')){
-                        null
-                    } else { filename }
-                },
-                pattern: '*.*'
+                } else { filename }
+              },
             ],
             [
                 path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/top_ranked_structures" },
diff --git a/nextflow.config b/nextflow.config
index 24ef5c55..06f6552f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -224,6 +224,7 @@ params {
     // Boilerplate options
     outdir                       = null
     publish_dir_mode             = 'copy'
+    save_base_output             = false
     email                        = null
     email_on_fail                = null
     plaintext_email              = false