diff --git a/CHANGELOG.md b/CHANGELOG.md
index f43c0e93..dc3cc074 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -102,6 +102,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #462](https://github.com/nf-core/proteinfold/pulls/462)] - Update publishdir patterns for RoseTTAFold-All-Atom modules
 - [[PR #464](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for Boltz module
 - [[PR #469](https://github.com/nf-core/proteinfold/pulls/454)] - HTML reports now in /reports output directory
+- [[PR #468](https://github.com/nf-core/proteinfold/pulls/468)] - Update publishdir patterns for Alphafold3 module
 
 ### Parameters
 
diff --git a/conf/modules_alphafold3.config b/conf/modules_alphafold3.config
index 32530d32..706a0252 100644
--- a/conf/modules_alphafold3.config
+++ b/conf/modules_alphafold3.config
@@ -92,9 +92,55 @@ process {
     withName: 'RUN_ALPHAFOLD3' {
         accelerator = params.use_gpu? 1 : 0
         publishDir = [
-            path: { "${params.outdir}/alphafold3" },
-            mode: 'copy',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            [
+                path: { "${params.outdir}/alphafold3/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_plddt.tsv'
+            ],
+            [
+                path: { "${params.outdir}/alphafold3/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_ptm.tsv'
+            ],
+            [
+                path: { "${params.outdir}/alphafold3/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_iptm.tsv'
+            ],
+            [
+                path: { "${params.outdir}/alphafold3/${meta.id}" },
+                mode: 'copy',
+                saveAs: { filename -> "paes/$filename" },
+                pattern: '*_pae.tsv'
+            ],
+            [
+                path: { "${params.outdir}/alphafold3/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_alphafold3_msa.tsv'
+            ],
+            [
+                enabled: params.save_intermediates,
+                path: { "${params.outdir}/alphafold3/${meta.id}/raw" },
+                mode: 'copy',
+                pattern: 'raw/**',
+                saveAs: { filename -> filename.toString().replaceFirst(/^raw\//, '') }
+            ],
+            [
+                path: { "${params.outdir}/alphafold3/top_ranked_structures" },
+                mode: 'copy',
+                saveAs: { "${meta.id}.cif" },
+                pattern: '*_alphafold3.cif'
+            ]
+        ]
+    }
+    withName: 'MMCIF2PDB_TOP_RANKED' {
+        publishDir = [
+            [
+                path: { "${params.outdir}/alphafold3/top_ranked_structures" },
+                mode: 'copy',
+                saveAs: { "${meta.id}.pdb" },
+                pattern: '*.pdb'
+            ]
         ]
     }
 }
diff --git a/modules/local/mmcif2pdb/main.nf b/modules/local/mmcif2pdb/main.nf
index f83cc91e..e0a7c137 100644
--- a/modules/local/mmcif2pdb/main.nf
+++ b/modules/local/mmcif2pdb/main.nf
@@ -20,7 +20,7 @@ process MMCIF2PDB {
     """
     for mmcif in *.cif
     do
-        pdb_out=\$(basename "\$mmcif")
+        pdb_out=\$(basename "\$mmcif" .cif)
         mmcif_to_pdb.py \${mmcif} --pdb_out "\${pdb_out}.pdb"
     done
 
diff --git a/modules/local/run_alphafold3/main.nf b/modules/local/run_alphafold3/main.nf
index 3ed38242..738465c7 100644
--- a/modules/local/run_alphafold3/main.nf
+++ b/modules/local/run_alphafold3/main.nf
@@ -18,11 +18,14 @@ process RUN_ALPHAFOLD3 {
     path "uniprot/*"
 
     output:
-    tuple val(meta), path ("publish/*alphafold3.cif")       , emit: top_ranked_cif
-    tuple val(meta), path ("publish/*ranked_*.cif")         , emit: cif
+    path ("raw/**")                                         , emit: raw
+    tuple val(meta), path ("${meta.id}_alphafold3.cif")     , emit: top_ranked_cif
+    tuple val(meta), path ("raw/*ranked_*.cif")             , emit: cif
     tuple val(meta), path ("${meta.id}_plddt.tsv")          , emit: multiqc
     tuple val(meta), path ("${meta.id}_alphafold3_msa.tsv") , emit: msa
     tuple val(meta), path ("${meta.id}_0_pae.tsv")          , emit: pae
+    tuple val(meta), path ("${meta.id}_ptm.tsv")            , emit: ptms
+    tuple val(meta), path ("${meta.id}_iptm.tsv")           , optional: true, emit: iptms
     path "versions.yml"                                     , emit: versions
 
     when:
@@ -38,33 +41,30 @@ process RUN_ALPHAFOLD3 {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def af3_id = meta.id.toLowerCase()
     """
-    for f in ./pdb_seqres/pdb_seqres.txt ./pdb_seqres/pdb_seqres_2022_09_28.fasta; do
-	    if [[ -f \$f ]]; then
-            pdb_seqres=\$f
-            break
-        fi
-    done
+    # Check database files exist and set variables
+    pdb_seqres=\$(ls -v ./pdb_seqres/pdb_seqres.txt ./pdb_seqres/pdb_seqres_2022_09_28.fasta 2>/dev/null | tail -n 1 || echo "")
+    if [[ -z "\$pdb_seqres" ]]; then
+        echo "ERROR: No pdb_seqres file found"
+        exit 1
+    fi
 
-    for f in ./uniref90/uniref90*.fa ./uniref90/uniref90*.fasta; do
-    	if [[ -f \$f ]]; then
-            uniref90=\$f
-            break
-    	fi
-    done
+    uniref90=\$(ls -v ./uniref90/uniref90*.fa ./uniref90/uniref90*.fasta 2>/dev/null | tail -n 1 || echo "")
+    if [[ -z "\$uniref90" ]]; then
+        echo "ERROR: No uniref90 file found"
+        exit 1
+    fi
 
-    for f in ./mgnify/mgy_clusters*.fa ./mgnify/mgnify_clusters*.fasta; do
-        if [[ -f \$f ]]; then
-            mgnify=\$f
-            break
-        fi
-    done
+    mgnify=\$(ls -v ./mgnify/mgy_clusters*.fa ./mgnify/mgnify_clusters*.fasta 2>/dev/null | tail -n 1 || echo "")
+    if [[ -z "\$mgnify" ]]; then
+        echo "ERROR: No mgnify file found"
+        exit 1
+    fi
 
-    for f in ./uniprot/uniprot.fasta ./uniprot/uniprot*.fa; do
-        if [[ -f \$f ]]; then
-            uniprot=\$f
-            break
-        fi
-    done
+    uniprot=\$(ls -v ./uniprot/uniprot.fasta ./uniprot/uniprot*.fa 2>/dev/null | tail -n 1 || echo "")
+    if [[ -z "\$uniprot" ]]; then
+        echo "ERROR: No uniprot file found"
+        exit 1
+    fi
 
     python3 /app/alphafold/run_alphafold.py \\
         --json_path=${json} \\
@@ -78,32 +78,34 @@ process RUN_ALPHAFOLD3 {
         --output_dir=\$PWD \\
         $args
 
-    ## Rename the top ranked model
-    if [ ! -d publish ]; then
-        mkdir -p publish
-    fi
-
-    ## Move the rest of the models and rename them according to their rank
+    ### Move the rest of the models and rename them according to their rank
     name=\$(jq -r '.name' ${json})
-    cp -n "\${name}/\${name}_model.cif" "publish/${prefix}_alphafold3.cif"
+
+    ## Copy top ranked model to root
+    cp -n "\${name}/\${name}_model.cif" "${prefix}_alphafold3.cif"
 
     ## Sort the rows by ranking_score in descending order
     sorted_csv=\$(head -n 1 "\${name}/ranking_scores.csv"; tail -n +2 "\${name}/ranking_scores.csv" | sort -t, -k3 -nr)
     rank=0
-    touch publish/combined_plddt_mqc.tsv
 
-    ## Generate files with rank tag
+    ## Create raw directory for intermediate files
+    mkdir -p raw
+
+    ## Generate files with rank tag in raw directory
     echo "\$sorted_csv" | tail -n +2 | while IFS=',' read -r seed sample ranking_score; do
-    cp -n "\${name}/seed-\${seed}_sample-\${sample}/model.cif" "publish/seed_\${seed}_sample_\${sample}_ranked_\${rank}.cif"
+    cp -n "\${name}/seed-\${seed}_sample-\${sample}/model.cif" "raw/seed_\${seed}_sample_\${sample}_ranked_\${rank}.cif"
     rank=\$((rank + 1))
     done
 
     extract_metrics.py --name ${prefix} \\
         --jsons ${af3_id}/${af3_id}_data.json ${af3_id}/${af3_id}_summary_confidences.json ${af3_id}/${af3_id}_confidences.json \\
-        --structs publish/*ranked_*.cif
+        --structs raw/*ranked_*.cif
 
     mv "${prefix}_msa.tsv" "${meta.id}_alphafold3_msa.tsv"
 
+    ## Move alphafold3 output directory to raw for save_intermediates
+    mv \${name}/* raw/
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         python: \$(python3 --version | sed 's/Python //g')
@@ -113,16 +115,18 @@ process RUN_ALPHAFOLD3 {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    mkdir publish
-    touch publish/${prefix}_alphafold3.cif
-    touch publish/${prefix}_ranked_1.cif
-    touch publish/${prefix}_ranked_2.cif
-    touch publish/${prefix}_ranked_3.cif
-    touch publish/${prefix}_ranked_4.cif
-    touch publish/${prefix}_ranked_5.cif
+    mkdir -p raw
+    touch ${prefix}_alphafold3.cif
+    touch raw/${prefix}_ranked_1.cif
+    touch raw/${prefix}_ranked_2.cif
+    touch raw/${prefix}_ranked_3.cif
+    touch raw/${prefix}_ranked_4.cif
+    touch raw/${prefix}_ranked_5.cif
     touch ${prefix}_plddt.tsv
     touch ${prefix}_alphafold3_msa.tsv
     touch ${prefix}_0_pae.tsv
+    touch ${prefix}_ptm.tsv
+    touch ${prefix}_iptm.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/alphafold2_download.nf.test.snap b/tests/alphafold2_download.nf.test.snap
index 901df40d..d13e433f 100644
--- a/tests/alphafold2_download.nf.test.snap
+++ b/tests/alphafold2_download.nf.test.snap
@@ -64,16 +64,14 @@
                 "alphafold2/standard/top_ranked_structures",
                 "alphafold2/standard/top_ranked_structures/T1024.pdb",
                 "alphafold2/standard/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multiqc",
                 "multiqc/alphafold2_multiqc_data",
                 "multiqc/alphafold2_multiqc_plots",
                 "multiqc/alphafold2_multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "bfd-first_non_consensus_sequences.fasta:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -107,16 +105,14 @@
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "alphafold2_multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "alphafold2_multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-29T21:35:56.027817716"
+        "timestamp": "2026-02-12T10:46:14.365206"
     }
 }
\ No newline at end of file
diff --git a/tests/alphafold2_split.nf.test.snap b/tests/alphafold2_split.nf.test.snap
index 917420c5..c5c932ac 100644
--- a/tests/alphafold2_split.nf.test.snap
+++ b/tests/alphafold2_split.nf.test.snap
@@ -45,16 +45,14 @@
                 "alphafold2/split_msa_prediction/top_ranked_structures",
                 "alphafold2/split_msa_prediction/top_ranked_structures/T1024.pdb",
                 "alphafold2/split_msa_prediction/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multiqc",
                 "multiqc/alphafold2_multiqc_data",
                 "multiqc/alphafold2_multiqc_plots",
                 "multiqc/alphafold2_multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "T1024_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -67,16 +65,14 @@
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "alphafold2_multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "alphafold2_multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-29T21:36:12.286799433"
+        "timestamp": "2026-02-12T10:47:42.40387"
     }
 }
\ No newline at end of file
diff --git a/tests/alphafold3.nf.test.snap b/tests/alphafold3.nf.test.snap
index 7d53d465..63cfd43d 100644
--- a/tests/alphafold3.nf.test.snap
+++ b/tests/alphafold3.nf.test.snap
@@ -25,40 +25,34 @@
             },
             [
                 "alphafold3",
-                "alphafold3/T1024_0_pae.tsv",
-                "alphafold3/T1024_alphafold3_msa.tsv",
-                "alphafold3/T1024_plddt.tsv",
-                "alphafold3/T1026_0_pae.tsv",
-                "alphafold3/T1026_alphafold3_msa.tsv",
-                "alphafold3/T1026_plddt.tsv",
-                "alphafold3/publish",
-                "alphafold3/publish/T1024_alphafold3.cif",
-                "alphafold3/publish/T1024_ranked_1.cif",
-                "alphafold3/publish/T1024_ranked_2.cif",
-                "alphafold3/publish/T1024_ranked_3.cif",
-                "alphafold3/publish/T1024_ranked_4.cif",
-                "alphafold3/publish/T1024_ranked_5.cif",
-                "alphafold3/publish/T1026_alphafold3.cif",
-                "alphafold3/publish/T1026_ranked_1.cif",
-                "alphafold3/publish/T1026_ranked_2.cif",
-                "alphafold3/publish/T1026_ranked_3.cif",
-                "alphafold3/publish/T1026_ranked_4.cif",
-                "alphafold3/publish/T1026_ranked_5.cif",
+                "alphafold3/T1024",
+                "alphafold3/T1024/T1024_alphafold3_msa.tsv",
+                "alphafold3/T1024/T1024_iptm.tsv",
+                "alphafold3/T1024/T1024_plddt.tsv",
+                "alphafold3/T1024/T1024_ptm.tsv",
+                "alphafold3/T1024/paes",
+                "alphafold3/T1024/paes/T1024_0_pae.tsv",
+                "alphafold3/T1026",
+                "alphafold3/T1026/T1026_alphafold3_msa.tsv",
+                "alphafold3/T1026/T1026_iptm.tsv",
+                "alphafold3/T1026/T1026_plddt.tsv",
+                "alphafold3/T1026/T1026_ptm.tsv",
+                "alphafold3/T1026/paes",
+                "alphafold3/T1026/paes/T1026_0_pae.tsv",
+                "alphafold3/top_ranked_structures",
+                "alphafold3/top_ranked_structures/T1024.cif",
+                "alphafold3/top_ranked_structures/T1024.pdb",
+                "alphafold3/top_ranked_structures/T1026.cif",
+                "alphafold3/top_ranked_structures/T1026.pdb",
                 "fasta",
                 "fasta/T1024.json",
                 "fasta/T1026.json",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "mmcif2pdb",
-                "mmcif2pdb/T1024_alphafold3.cif.pdb",
                 "mmcif2pdb/T1024_ranked_1.cif.pdb",
                 "mmcif2pdb/T1024_ranked_2.cif.pdb",
                 "mmcif2pdb/T1024_ranked_3.cif.pdb",
                 "mmcif2pdb/T1024_ranked_4.cif.pdb",
                 "mmcif2pdb/T1024_ranked_5.cif.pdb",
-                "mmcif2pdb/T1026_alphafold3.cif.pdb",
                 "mmcif2pdb/T1026_ranked_1.cif.pdb",
                 "mmcif2pdb/T1026_ranked_2.cif.pdb",
                 "mmcif2pdb/T1026_ranked_3.cif.pdb",
@@ -69,50 +63,44 @@
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
-                "T1024_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_alphafold3_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1024_iptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1024_ptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1024_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_alphafold3_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026_iptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_alphafold3.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_ranked_1.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_ranked_2.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_ranked_3.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_ranked_4.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_ranked_5.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_alphafold3.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_ranked_1.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_ranked_2.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_ranked_3.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_ranked_4.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_ranked_5.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026_ptm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1024.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026.cif:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.json:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.json:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1024_alphafold3.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_ranked_1.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_ranked_2.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_ranked_3.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_ranked_4.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_ranked_5.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_alphafold3.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_ranked_1.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_ranked_2.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_ranked_3.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_ranked_4.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_ranked_5.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "T1026_ranked_5.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-13T14:35:17.692615"
+        "timestamp": "2026-02-12T10:20:34.770288"
     }
 }
\ No newline at end of file
diff --git a/tests/colabfold_download.nf.test.snap b/tests/colabfold_download.nf.test.snap
index 22831612..27424a83 100644
--- a/tests/colabfold_download.nf.test.snap
+++ b/tests/colabfold_download.nf.test.snap
@@ -41,10 +41,6 @@
                 "colabfold/top_ranked_structures",
                 "colabfold/top_ranked_structures/T1024.pdb",
                 "colabfold/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multifasta",
                 "multifasta/input.csv",
                 "multiqc",
@@ -52,7 +48,9 @@
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 [
@@ -68,16 +66,14 @@
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-30T21:28:32.731283423"
+        "timestamp": "2026-02-12T10:48:56.591432"
     }
 }
\ No newline at end of file
diff --git a/tests/colabfold_local.nf.test.snap b/tests/colabfold_local.nf.test.snap
index e3202e7f..4f6e1fbf 100644
--- a/tests/colabfold_local.nf.test.snap
+++ b/tests/colabfold_local.nf.test.snap
@@ -39,10 +39,6 @@
                 "colabfold/top_ranked_structures",
                 "colabfold/top_ranked_structures/T1024.pdb",
                 "colabfold/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multifasta",
                 "multifasta/input.csv",
                 "multiqc",
@@ -50,7 +46,9 @@
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "T1024_colabfold_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -63,16 +61,14 @@
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-30T21:28:47.156766004"
+        "timestamp": "2026-02-12T10:50:01.242169"
     }
 }
\ No newline at end of file
diff --git a/tests/colabfold_webserver.nf.test.snap b/tests/colabfold_webserver.nf.test.snap
index b2772aed..9cfb08cb 100644
--- a/tests/colabfold_webserver.nf.test.snap
+++ b/tests/colabfold_webserver.nf.test.snap
@@ -35,10 +35,6 @@
                 "colabfold/top_ranked_structures",
                 "colabfold/top_ranked_structures/T1024.pdb",
                 "colabfold/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multifasta",
                 "multifasta/input.csv",
                 "multiqc",
@@ -46,7 +42,9 @@
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "T1024_colabfold_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -59,16 +57,14 @@
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-30T21:29:00.639422387"
+        "timestamp": "2026-02-12T10:51:03.271168"
     }
 }
\ No newline at end of file
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 57347ffb..73d2f7b7 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -38,16 +38,14 @@
                 "alphafold2/standard/top_ranked_structures",
                 "alphafold2/standard/top_ranked_structures/T1024.pdb",
                 "alphafold2/standard/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multiqc",
                 "multiqc/alphafold2_multiqc_data",
                 "multiqc/alphafold2_multiqc_plots",
                 "multiqc/alphafold2_multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "T1024_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -62,16 +60,14 @@
                 "T1026_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "alphafold2_multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "alphafold2_multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-29T21:37:26.752545973"
+        "timestamp": "2026-02-12T10:52:01.757925"
     }
 }
\ No newline at end of file
diff --git a/tests/esmfold.nf.test.snap b/tests/esmfold.nf.test.snap
index 82942a64..9c5906d8 100644
--- a/tests/esmfold.nf.test.snap
+++ b/tests/esmfold.nf.test.snap
@@ -24,16 +24,14 @@
                 "esmfold/default/top_ranked_structures",
                 "esmfold/default/top_ranked_structures/T1024.pdb",
                 "esmfold/default/top_ranked_structures/T1026.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multiqc",
                 "multiqc/multiqc_data",
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "T1024_esmfold.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -42,15 +40,13 @@
                 "T1026_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-13T14:39:38.718156"
+        "timestamp": "2026-02-12T11:20:57.334392"
     }
 }
\ No newline at end of file
diff --git a/tests/split_fasta.nf.test.snap b/tests/split_fasta.nf.test.snap
index fb154701..d60e412b 100644
--- a/tests/split_fasta.nf.test.snap
+++ b/tests/split_fasta.nf.test.snap
@@ -39,10 +39,6 @@
                 "colabfold/top_ranked_structures",
                 "colabfold/top_ranked_structures/H1065_N4-Cytosine_Methyltransferase_Serratia_marcescens_subunit_1_127_residues.pdb",
                 "colabfold/top_ranked_structures/H1065_N4-Cytosine_Methyltransferase_Serratia_marcescens_subunit_2_98_residues.pdb",
-                "generate",
-                "generate/test_LDDT.html",
-                "generate/test_alphafold2_report.html",
-                "generate/test_seq_coverage.png",
                 "multifasta",
                 "multifasta/input.csv",
                 "multiqc",
@@ -50,7 +46,9 @@
                 "multiqc/multiqc_plots",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml"
+                "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
+                "reports",
+                "reports/test_alphafold2_report.html"
             ],
             [
                 "H1065_N4-Cytosine_Methyltransferase_Serratia_marcescens_subunit_1_127_residues_colabfold_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -63,16 +61,14 @@
                 "H1065_N4-Cytosine_Methyltransferase_Serratia_marcescens_subunit_2_98_residues_0_pae.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "H1065_N4-Cytosine_Methyltransferase_Serratia_marcescens_subunit_1_127_residues.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "H1065_N4-Cytosine_Methyltransferase_Serratia_marcescens_subunit_2_98_residues.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_LDDT.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_seq_coverage.png:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "input.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2026-01-30T21:29:42.953076263"
+        "timestamp": "2026-02-12T11:33:41.854887"
     }
 }
\ No newline at end of file