nf-core · JoseEspinosa · Feb 12, 2026 · Feb 12, 2026 · Feb 12, 2026 · Feb 12, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -104,6 +104,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #466](https://github.com/nf-core/proteinfold/pulls/464)] - Update module conf and publishdir patterns for ESMFold, pass through container args
 - [[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
+- [[PR #471](https://github.com/nf-core/proteinfold/pulls/471)] - Update publishdir patterns for Rosettafold2na module
 
 ### Parameters
 

diff --git a/conf/modules_rosettafold2na.config b/conf/modules_rosettafold2na.config
@@ -22,18 +22,35 @@ process {
     withName: 'RUN_ROSETTAFOLD2NA' {
         accelerator = params.use_gpu? 1 : 0
         publishDir = [
-            path: { "${params.outdir}/rosettafold2na/" },
-            mode: 'copy',
-            saveAs: { filename ->
-                if (filename.endsWith('_pae.tsv')) {
-                    "paes/$filename"
-                } else if (filename.equals('versions.yml')) {
-                    null
-                } else {
-                    filename
-                }
-            },
-            pattern: '*.*'
+            [
+                path: { "${params.outdir}/rosettafold2na/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_plddt.tsv'
+            ],
+            [
+                path: { "${params.outdir}/rosettafold2na/${meta.id}" },
+                mode: 'copy',
+                saveAs: { filename -> "paes/$filename" },
+                pattern: '*_pae.tsv'
+            ],
+            [
+                path: { "${params.outdir}/rosettafold2na/${meta.id}" },
+                mode: 'copy',
+                pattern: '*_rosettafold2na_msa.tsv'
+            ],
+            [
+                enabled: params.save_intermediates,
+                path: { "${params.outdir}/rosettafold2na/${meta.id}/raw" },
+                mode: 'copy',
+                pattern: 'raw/**',
+                saveAs: { filename -> filename.toString().replaceFirst(/^raw\//, '') }
+            ],
+            [
+                path: { "${params.outdir}/rosettafold2na/top_ranked_structures" },
+                mode: 'copy',
+                saveAs: { "${meta.id}.pdb" },
+                pattern: '*_rosettafold2na.pdb'
+            ]
         ]
     }
 

diff --git a/modules/local/run_rosettafold2na/main.nf b/modules/local/run_rosettafold2na/main.nf
@@ -17,11 +17,13 @@ process RUN_ROSETTAFOLD2NA {
     path ('network/weights/*')
 
     output:
-    tuple val(meta), path("${meta.id}_rf2na.pdb"), emit: pdb
-    tuple val(meta), path("${meta.id}_plddt_mqc.tsv"), emit: multiqc
-    tuple val(meta), path("${meta.id}_rosettafold2na_msa.tsv"), emit: msa
-    tuple val(meta), path("${meta.id}_0_pae.tsv"), emit: pae
-    path "versions.yml", emit: versions
+    path ("raw/**")                                            , emit: raw
+    tuple val(meta), path("${meta.id}_rosettafold2na.pdb")     , emit: top_ranked_pdb
+    tuple val(meta), path("raw/*.pdb")                         , emit: pdb
+    tuple val(meta), path("${meta.id}_plddt.tsv")              , emit: multiqc
+    tuple val(meta), path("${meta.id}_rosettafold2na_msa.tsv") , emit: msa
+    tuple val(meta), path("${meta.id}_0_pae.tsv")              , emit: pae
+    path "versions.yml"                                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -67,7 +69,12 @@ process RUN_ROSETTAFOLD2NA {
 
     ./run_RF2NA.sh ${meta.id}_rf2na_output "\${chain_args[@]}"
 
-    cp ${meta.id}_rf2na_output/models/model_00.pdb ./${meta.id}_rf2na.pdb
+    ## Create raw directory for intermediate files
+    mkdir -p raw
+
+    ## Copy top ranked model to root and raw
+    cp ${meta.id}_rf2na_output/models/model_00.pdb ./${meta.id}_rosettafold2na.pdb
+    cp ${meta.id}_rf2na_output/models/*.pdb raw/
 
     # Extract PAE matrix from NPZ and save as TSV for reporting
     /conda/envs/RF2NA/bin/python3 - <<'PY' "${meta.id}_rf2na_output/models/model_00.npz" "${meta.id}_0_pae.tsv"
@@ -81,36 +88,32 @@ PY
     extract_metrics.py --name ${meta.id} \
         --structs "${meta.id}_rf2na_output/models/model_00.pdb" ${'$'}A3M_ARGS
 
-    mv "${meta.id}_plddt.tsv" "${meta.id}_plddt_mqc.tsv"
-    if [ -f "${meta.id}_msa.tsv" ]; then
-        mv "${meta.id}_msa.tsv" "${meta.id}_rosettafold2na_msa.tsv"
-    fi
+    mv "${meta.id}_msa.tsv" "${meta.id}_rosettafold2na_msa.tsv"
 
-    printf '"%s":\n  python: %s\n' \
-        "${task.process}" \
-        "\$(/conda/envs/RF2NA/bin/python3 --version | sed 's/Python //g')" > versions.yml
+    ## Move rf2na output directory to raw for save_intermediates
+    mv ${meta.id}_rf2na_output/* raw/
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        rosettafold2na: $VERSION
-    END_VERSIONS
+cat <<-END_VERSIONS > versions.yml
+"${task.process}":
+    python: \$(python3 --version | sed 's/Python //g')
+    rosettafold2na: "${VERSION}"
+END_VERSIONS
     """
 
     stub:
     def VERSION = 'v0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
-    touch "${meta.id}_rf2na.pdb"
-    touch "${meta.id}_plddt_mqc.tsv"
+    mkdir -p raw
+    touch "${meta.id}_rosettafold2na.pdb"
+    touch raw/model_00.pdb
+    touch "${meta.id}_plddt.tsv"
     touch "${meta.id}_0_pae.tsv"
     touch "${meta.id}_rosettafold2na_msa.tsv"
 
-    printf '"%s":\n  python: %s\n' \
-        "${task.process}" \
-        "\$(/conda/envs/RF2NA/bin/python3 --version | sed 's/Python //g')" > versions.yml
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        rosettafold2na: $VERSION
+        python: \$(python3 --version | sed 's/Python //g')
+        rosettafold2na: "${VERSION}"
     END_VERSIONS
     """
 }
diff --git a/tests/esmfold.nf.test.snap b/tests/esmfold.nf.test.snap
@@ -16,14 +16,13 @@
             },
             [
                 "esmfold",
-                "esmfold/default",
-                "esmfold/default/T1024_esmfold.pdb",
-                "esmfold/default/T1024_plddt.tsv",
-                "esmfold/default/T1026_esmfold.pdb",
-                "esmfold/default/T1026_plddt.tsv",
-                "esmfold/default/top_ranked_structures",
-                "esmfold/default/top_ranked_structures/T1024.pdb",
-                "esmfold/default/top_ranked_structures/T1026.pdb",
+                "esmfold/T1024",
+                "esmfold/T1024/T1024_plddt.tsv",
+                "esmfold/T1026",
+                "esmfold/T1026/T1026_plddt.tsv",
+                "esmfold/top_ranked_structures",
+                "esmfold/top_ranked_structures/T1024.pdb",
+                "esmfold/top_ranked_structures/T1026.pdb",
                 "multiqc",
                 "multiqc/multiqc_data",
                 "multiqc/multiqc_plots",
@@ -34,9 +33,7 @@
                 "reports/test_alphafold2_report.html"
             ],
             [
-                "T1024_esmfold.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "T1026_esmfold.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026_plddt.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1024.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -45,8 +42,8 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-02-12T11:20:57.334392"
+        "timestamp": "2026-02-12T18:09:13.544553"
     }
 }