nf-core · JoseEspinosa · Feb 5, 2026 · Jan 29, 2026 · Jan 29, 2026 · Jan 30, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -91,6 +91,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #451](https://github.com/nf-core/proteinfold/pulls/451)] - Remove af2 multimer padding from msa plots.
 - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Add `boltz_use_kernels` parameter to enable/disable using optimized Triton-based CUDA kernels CUDA kernels for Boltz inference.
 - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Handle incompatible CUDA kernel errors in Boltz by automatically retrying with `--no_kernels` false.
+- [[PR #454](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for alphafold2 modules
 
 ### Parameters
 

diff --git a/conf/modules_alphafold2.config b/conf/modules_alphafold2.config
@@ -60,11 +60,15 @@ process {
                 saveAs: { filename ->
                     if(filename.endsWith('_pae.tsv')){
                         "paes/$filename"
-                    } else if(filename.equals('versions.yml')){
-                        null
                     } else { filename }
                 },
-                pattern: '*.*'
+                pattern: '*.tsv'
+            ],
+            [
+                enabled: params.save_intermediates,
+                path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}/" },
+                mode: 'copy',
+                pattern: 'raw/**'
             ],
             [
                 path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/top_ranked_structures" },
@@ -80,27 +84,50 @@ process {
     withName: 'RUN_ALPHAFOLD2_MSA' {
         ext.args =  params.alphafold2_max_template_date ? "--max_template_date ${params.alphafold2_max_template_date}" : ''
         publishDir = [
-            path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}" },
-            mode: 'copy',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            [
+                path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}/msa/" },
+                mode: 'copy',
+                pattern: 'raw/*.*',
+                saveAs: { filename ->
+                    if(filename.equals('versions.yml')) {
+                        null
+                    } else {
+                        filename.toString().replaceFirst(/^raw\//, '')
+                    }
+                }
+            ],
+            [
+                enabled: params.save_intermediates,
+                path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}/raw/" },
+                mode: 'copy',
+                pattern: 'raw/msas/**',
+                saveAs: { filename -> filename.toString().replaceFirst(/^raw\//, '') }
+            ]
         ]
     }
 
     withName: 'RUN_ALPHAFOLD2_PRED' {
         accelerator = params.use_gpu? 1 : 0
-        ext.args   = params.use_gpu ? '--use_gpu_relax=true' : '--use_gpu_relax=false'
+        ext.args   = [
+            params.use_gpu ? '--use_gpu_relax=true' : '--use_gpu_relax=false',
+            params.alphafold2_random_seed ? "--random_seed=${params.alphafold2_random_seed}" : ''
+        ].join(' ').trim()
         publishDir = [
             [
                 path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}" },
                 mode: 'copy',
                 saveAs: { filename ->
                     if(filename.endsWith('_pae.tsv')){
                         "paes/$filename"
-                    } else if(filename.equals('versions.yml')){
-                        null
                     } else { filename }
                 },
-                pattern: '*.*'
+                pattern: '*.tsv'
+            ],
+            [
+                enabled: params.save_intermediates,
+                path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/${meta.id}/" },
+                mode: 'copy',
+                pattern: 'raw/**'
             ],
             [
                 path: { "${params.outdir}/alphafold2/${params.alphafold2_mode}/top_ranked_structures" },

diff --git a/modules/local/run_alphafold2/main.nf b/modules/local/run_alphafold2/main.nf
@@ -26,9 +26,9 @@ process RUN_ALPHAFOLD2 {
     path ('uniprot/*')
 
     output:
-    path ("${fasta.baseName}*")
+    path ("raw/**")                                         , emit: raw
     tuple val(meta), path ("${meta.id}_alphafold2.pdb")     , emit: top_ranked_pdb
-    tuple val(meta), path ("${fasta.baseName}/ranked*.pdb") , emit: pdb
+    tuple val(meta), path ("raw/ranked*.pdb") , emit: pdb
     // TODO: re-label multiqc -> plddt so multiqc channel can take in all metrics
     tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
     tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv") , emit: msa
@@ -83,6 +83,9 @@ process RUN_ALPHAFOLD2 {
 
     mv "${meta.id}_msa.tsv" "${meta.id}_alphafold2_msa.tsv"
 
+    # Can't use fasta.baseName to batch outputs in publishDir
+    mv "${fasta.baseName}" raw/
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python3 --version | sed 's/Python //g')
@@ -102,12 +105,12 @@ process RUN_ALPHAFOLD2 {
     touch "${meta.id}_0_pae.tsv"
     touch "${meta.id}_ptm.tsv"
     touch "${meta.id}_iptm.tsv"
-    mkdir "${fasta.baseName}"
-    touch "${fasta.baseName}/ranked_0.pdb"
-    touch "${fasta.baseName}/ranked_1.pdb"
-    touch "${fasta.baseName}/ranked_2.pdb"
-    touch "${fasta.baseName}/ranked_3.pdb"
-    touch "${fasta.baseName}/ranked_4.pdb"
+    mkdir "raw"
+    touch "raw/ranked_0.pdb"
+    touch "raw/ranked_1.pdb"
+    touch "raw/ranked_2.pdb"
+    touch "raw/ranked_3.pdb"
+    touch "raw/ranked_4.pdb"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/run_alphafold2_msa/main.nf b/modules/local/run_alphafold2_msa/main.nf
@@ -25,9 +25,9 @@ process RUN_ALPHAFOLD2_MSA {
     path ('uniprot/*')
 
     output:
-    path ("${fasta.baseName}*")
-    tuple val(meta), path ("${fasta.baseName}/features.pkl"), emit: features
-    path "versions.yml"                                     , emit: versions
+    path ("raw/**")                           , emit: raw
+    tuple val(meta), path ("raw/features.pkl"), emit: features
+    path "versions.yml"                       , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -64,6 +64,9 @@ process RUN_ALPHAFOLD2_MSA {
         --obsolete_pdbs_path=./clean_obsolete.dat \
         $args
 
+    # Can't use fasta.baseName to batch outputs in publishDir
+    mv "${fasta.baseName}" raw/
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python3 --version | sed 's/Python //g')
@@ -75,8 +78,8 @@ process RUN_ALPHAFOLD2_MSA {
 
     stub:
     """
-    mkdir ./"${fasta.baseName}"
-    touch ./"${fasta.baseName}"/features.pkl
+    mkdir ./raw
+    touch ./raw/features.pkl
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/run_alphafold2_pred/main.nf b/modules/local/run_alphafold2_pred/main.nf
@@ -24,9 +24,9 @@ process RUN_ALPHAFOLD2_PRED {
     path ('uniprot/*')
 
     output:
-    path ("${fasta.baseName}*")
+    path ("raw/**")                                         , emit: raw
     tuple val(meta), path ("${meta.id}_alphafold2.pdb")     , emit: top_ranked_pdb
-    tuple val(meta), path ("${fasta.baseName}/ranked*.pdb") , emit: pdb
+    tuple val(meta), path ("raw/ranked*.pdb")               , emit: pdb
     tuple val(meta), path ("${meta.id}_alphafold2_msa.tsv") , emit: msa
     // TODO: re-label multiqc -> plddt so multiqc channel can take in all metrics
     tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
@@ -62,6 +62,9 @@ process RUN_ALPHAFOLD2_PRED {
 
     mv "${meta.id}_msa.tsv" "${meta.id}_alphafold2_msa.tsv"
 
+    # Can't use fasta.baseName to batch outputs in publishDir
+    mv "${fasta.baseName}" raw/
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python3 --version | sed 's/Python //g')
@@ -79,12 +82,12 @@ process RUN_ALPHAFOLD2_PRED {
     touch "${meta.id}_plddt.tsv"
     touch "${meta.id}_alphafold2_msa.tsv"
     touch "${meta.id}_0_pae.tsv"
-    mkdir "${fasta.baseName}"
-    touch "${fasta.baseName}/ranked_0.pdb"
-    touch "${fasta.baseName}/ranked_1.pdb"
-    touch "${fasta.baseName}/ranked_2.pdb"
-    touch "${fasta.baseName}/ranked_3.pdb"
-    touch "${fasta.baseName}/ranked_4.pdb"
+    mkdir "raw/"
+    touch "raw/ranked_0.pdb"
+    touch "raw/ranked_1.pdb"
+    touch "raw/ranked_2.pdb"
+    touch "raw/ranked_3.pdb"
+    touch "raw/ranked_4.pdb"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/nextflow.config b/nextflow.config
@@ -13,6 +13,7 @@ params {
     input                       = null
     mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, alphafold3, helixfold3, boltz, rosettafold2na}
     use_gpu                     = false
+    save_intermediates          = false
     split_fasta                 = false
     db                          = null
     full_dbs                    = false // true/false, globally sets full_dbs if not independently set

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -44,6 +44,11 @@
                     "description": "Run on CPUs (default) or GPUs",
                     "fa_icon": "fas fa-microchip"
                 },
+                "save_intermediates": {
+                    "type": "boolean",
+                    "description": "Keep raw intermediate files",
+                    "fa_icon": "fas fa-microchip"
+                },
                 "split_fasta": {
                     "type": "boolean",
                     "description": "Split input multi-fasta file in separated fasta files each of them containing one sequence to be folded",

diff --git a/tests/alphafold2_download.nf.test.snap b/tests/alphafold2_download.nf.test.snap
@@ -48,27 +48,13 @@
                 "alphafold2",
                 "alphafold2/standard",
                 "alphafold2/standard/T1024",
-                "alphafold2/standard/T1024/T1024.1",
-                "alphafold2/standard/T1024/T1024.1/ranked_0.pdb",
-                "alphafold2/standard/T1024/T1024.1/ranked_1.pdb",
-                "alphafold2/standard/T1024/T1024.1/ranked_2.pdb",
-                "alphafold2/standard/T1024/T1024.1/ranked_3.pdb",
-                "alphafold2/standard/T1024/T1024.1/ranked_4.pdb",
-                "alphafold2/standard/T1024/T1024_alphafold2.pdb",
                 "alphafold2/standard/T1024/T1024_alphafold2_msa.tsv",
                 "alphafold2/standard/T1024/T1024_iptm.tsv",
                 "alphafold2/standard/T1024/T1024_plddt.tsv",
                 "alphafold2/standard/T1024/T1024_ptm.tsv",
                 "alphafold2/standard/T1024/paes",
                 "alphafold2/standard/T1024/paes/T1024_0_pae.tsv",
                 "alphafold2/standard/T1026",
-                "alphafold2/standard/T1026/T1026.1",
-                "alphafold2/standard/T1026/T1026.1/ranked_0.pdb",
-                "alphafold2/standard/T1026/T1026.1/ranked_1.pdb",
-                "alphafold2/standard/T1026/T1026.1/ranked_2.pdb",
-                "alphafold2/standard/T1026/T1026.1/ranked_3.pdb",
-                "alphafold2/standard/T1026/T1026.1/ranked_4.pdb",
-                "alphafold2/standard/T1026/T1026_alphafold2.pdb",
                 "alphafold2/standard/T1026/T1026_alphafold2_msa.tsv",
                 "alphafold2/standard/T1026/T1026_iptm.tsv",
                 "alphafold2/standard/T1026/T1026_plddt.tsv",
@@ -109,23 +95,11 @@
                     "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "uniref90.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_0.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_1.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_3.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_4.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_alphafold2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_iptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_ptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_0.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_1.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_3.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_4.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_alphafold2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_iptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -140,9 +114,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-13T14:33:28.434588"
+        "timestamp": "2026-01-29T21:35:56.027817716"
     }
 }
diff --git a/tests/alphafold2_split.nf.test.snap b/tests/alphafold2_split.nf.test.snap
@@ -29,31 +29,17 @@
                 "alphafold2",
                 "alphafold2/split_msa_prediction",
                 "alphafold2/split_msa_prediction/T1024",
-                "alphafold2/split_msa_prediction/T1024.1",
-                "alphafold2/split_msa_prediction/T1024.1/features.pkl",
-                "alphafold2/split_msa_prediction/T1024/T1024.1",
-                "alphafold2/split_msa_prediction/T1024/T1024.1/ranked_0.pdb",
-                "alphafold2/split_msa_prediction/T1024/T1024.1/ranked_1.pdb",
-                "alphafold2/split_msa_prediction/T1024/T1024.1/ranked_2.pdb",
-                "alphafold2/split_msa_prediction/T1024/T1024.1/ranked_3.pdb",
-                "alphafold2/split_msa_prediction/T1024/T1024.1/ranked_4.pdb",
-                "alphafold2/split_msa_prediction/T1024/T1024_alphafold2.pdb",
                 "alphafold2/split_msa_prediction/T1024/T1024_alphafold2_msa.tsv",
                 "alphafold2/split_msa_prediction/T1024/T1024_plddt.tsv",
+                "alphafold2/split_msa_prediction/T1024/msa",
+                "alphafold2/split_msa_prediction/T1024/msa/features.pkl",
                 "alphafold2/split_msa_prediction/T1024/paes",
                 "alphafold2/split_msa_prediction/T1024/paes/T1024_0_pae.tsv",
                 "alphafold2/split_msa_prediction/T1026",
-                "alphafold2/split_msa_prediction/T1026.1",
-                "alphafold2/split_msa_prediction/T1026.1/features.pkl",
-                "alphafold2/split_msa_prediction/T1026/T1026.1",
-                "alphafold2/split_msa_prediction/T1026/T1026.1/ranked_0.pdb",
-                "alphafold2/split_msa_prediction/T1026/T1026.1/ranked_1.pdb",
-                "alphafold2/split_msa_prediction/T1026/T1026.1/ranked_2.pdb",
-                "alphafold2/split_msa_prediction/T1026/T1026.1/ranked_3.pdb",
-                "alphafold2/split_msa_prediction/T1026/T1026.1/ranked_4.pdb",
-                "alphafold2/split_msa_prediction/T1026/T1026_alphafold2.pdb",
                 "alphafold2/split_msa_prediction/T1026/T1026_alphafold2_msa.tsv",
                 "alphafold2/split_msa_prediction/T1026/T1026_plddt.tsv",
+                "alphafold2/split_msa_prediction/T1026/msa",
+                "alphafold2/split_msa_prediction/T1026/msa/features.pkl",
                 "alphafold2/split_msa_prediction/T1026/paes",
                 "alphafold2/split_msa_prediction/T1026/paes/T1026_0_pae.tsv",
                 "alphafold2/split_msa_prediction/top_ranked_structures",
@@ -71,25 +57,13 @@
                 "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
             ],
             [
-                "features.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_0.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_1.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_3.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_4.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_alphafold2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "features.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_0.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_1.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_3.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "ranked_4.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_alphafold2.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1024_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "features.pkl:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -100,9 +74,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-13T14:34:11.513463"
+        "timestamp": "2026-01-29T21:36:12.286799433"
     }
 }