nf-core · jscgh · May 28, 2026 · May 28, 2026 · May 29, 2026 · May 29, 2026
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
@@ -30,6 +30,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
+      - volume=80gb
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
       total_shards: ${{ steps.set-shards.outputs.total_shards }}
@@ -51,7 +52,7 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
           SKIP_SCIENTIFIC: "true"
         with:
-          max_shards: 7
+          max_shards: 15
 
       - name: debug
         run: |
@@ -65,6 +66,7 @@ jobs:
     runs-on: # use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
+      - volume=80gb
     strategy:
       fail-fast: false
       matrix:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#586](https://github.com/nf-core/proteinfold/pull/586)] - Allow local msa for Boltz with non-protein entities.
 - [[#618](https://github.com/nf-core/proteinfold/pull/618)] - Resolve boltz `ext.args` in closure.
 - [[PR #626](https://github.com/nf-core/proteinfold/pull/618)] - Move scientific validation tests and BioPython setup to manual workflow.
+- [[#365](https://github.com/nf-core/proteinfold/issues/365)] - Run nf-tests with module containers so captured versions match.
 
 | Old parameter              | New parameter   |
 | -------------------------- | --------------- |

diff --git a/conf/test.config b/conf/test.config
@@ -31,9 +31,3 @@ params {
     input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
     alphafold2_db   = "${projectDir}/assets/dummy_db_dir"
 }
-
-process {
-    withName: 'RUN_ALPHAFOLD2' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_alphafold3_download.config b/conf/test_alphafold3_download.config
@@ -30,9 +30,3 @@ params {
     input                  = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
     alphafold3_params_path = "${projectDir}/assets/dummy_db_dir"
 }
-
-process {
-    withName: 'ARIA2|UNTAR|DOWNLOAD_PDBMMCIF_AF3|RUN_ALPHAFOLD3' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_alphafold3_standard.config b/conf/test_alphafold3_standard.config
@@ -30,9 +30,3 @@ params {
     input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
     alphafold3_db   = "${projectDir}/assets/dummy_db_dir"
 }
-
-process {
-    withName: 'RUN_ALPHAFOLD3_INFERENCE|RUN_ALPHAFOLD3_DATAPIPELINE' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_alphafold_download.config b/conf/test_alphafold_download.config
@@ -30,9 +30,3 @@ params {
     alphafold2_mode = 'standard'
     input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'ARIA2|UNTAR|RUN_ALPHAFOLD2' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_alphafold_split.config b/conf/test_alphafold_split.config
@@ -31,9 +31,3 @@ params {
     input           = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
     alphafold2_db   = "${projectDir}/assets/dummy_db_dir"
 }
-
-process {
-    withName: 'RUN_ALPHAFOLD2_MSA|RUN_ALPHAFOLD2_PRED' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_boltz.config b/conf/test_boltz.config
@@ -30,9 +30,3 @@ params {
     colabfold_db            = "${projectDir}/assets/dummy_db_dir"
     boltz_db                = "${projectDir}/assets/dummy_db_dir"
 }
-
-process {
-    withName: 'MMSEQS_COLABFOLDSEARCH|RUN_BOLTZ' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_colabfold_download.config b/conf/test_colabfold_download.config
@@ -30,9 +30,3 @@ params {
     use_msa_server   = true
     input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'ARIA2|UNTAR|COLABFOLD_BATCH' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_colabfold_local.config b/conf/test_colabfold_local.config
@@ -28,9 +28,3 @@ params {
     colabfold_db     = "${projectDir}/assets/dummy_db_dir"
     input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'MMSEQS_COLABFOLDSEARCH|COLABFOLD_BATCH' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_colabfold_webserver.config b/conf/test_colabfold_webserver.config
@@ -29,9 +29,3 @@ params {
     colabfold_db     = "${projectDir}/assets/dummy_db_dir"
     input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'COLABFOLD_BATCH' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_esmfold.config b/conf/test_esmfold.config
@@ -28,9 +28,3 @@ params {
     esmfold_db       = "${projectDir}/assets/dummy_db_dir"
     input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'RUN_ESMFOLD' {
-        container = 'quay.io/biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_helixfold3.config b/conf/test_helixfold3.config
@@ -28,9 +28,3 @@ params {
     helixfold3_db = "${projectDir}/assets/dummy_db_dir"
     input         = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'RUN_HELIXFOLD3' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_rosettafold2na.config b/conf/test_rosettafold2na.config
@@ -28,9 +28,3 @@ params {
     rosettafold2na_db    = "${projectDir}/assets/dummy_db_dir"
     input                = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/rna_complex_samplesheet.csv'
 }
-
-process {
-    withName: 'RUN_ROSETTAFOLD2NA' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_rosettafold_all_atom.config b/conf/test_rosettafold_all_atom.config
@@ -28,9 +28,3 @@ params {
     rosettafold_all_atom_db = "${projectDir}/assets/dummy_db_dir"
     input                   = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet.csv'
 }
-
-process {
-    withName: 'RUN_ROSETTAFOLD_ALL_ATOM' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/conf/test_split_fasta.config b/conf/test_split_fasta.config
@@ -29,9 +29,3 @@ params {
     colabfold_db     = "${projectDir}/assets/dummy_db_dir"
     input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v2.0/samplesheet_multimer.csv'
 }
-
-process {
-    withName: 'MMSEQS_COLABFOLDSEARCH|COLABFOLD_BATCH' {
-        container = 'biocontainers/gawk:5.1.0'
-    }
-}
diff --git a/modules/local/compare_structures/main.nf b/modules/local/compare_structures/main.nf
@@ -41,7 +41,7 @@ process COMPARE_STRUCTURES {
 
     stub:
     """
-    touch test_alphafold2_report.html
+    touch ${meta.id}_comparison_report.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/generate_report/main.nf b/modules/local/generate_report/main.nf
@@ -47,9 +47,9 @@ process GENERATE_REPORT {
 
     stub:
     """
-    touch test_alphafold2_report.html
-    touch test_seq_coverage.png
-    touch test_LDDT.html
+    touch ${meta.id}_${meta.model}_report.html
+    touch ${meta.id}_${meta.model}_seq_coverage.png
+    touch ${meta.id}_coverage_LDDT.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
diff --git a/tests/alphafold2_download.nf.test.snap b/tests/alphafold2_download.nf.test.snap
@@ -4,10 +4,10 @@
             25,
             {
                 "ARIA2": {
-                    "aria2": null
+                    "aria2": "1.36.0"
                 },
                 "ARIA2_PDB_SEQRES": {
-                    "aria2": null
+                    "aria2": "1.36.0"
                 },
                 "COMBINE_UNIPROT": {
                     "sed": 4.7
@@ -21,12 +21,12 @@
                     "generate_report.py": "Python 3.12.7"
                 },
                 "RUN_ALPHAFOLD2": {
-                    "python": "unknown",
+                    "python": "3.11.14",
                     "alphafold2": "unknown",
-                    "jax": "unknown",
-                    "jaxlib": "unknown",
-                    "numpy": "unknown",
-                    "biopython": "unknown"
+                    "jax": "0.4.26",
+                    "jaxlib": "0.4.26",
+                    "numpy": "1.24.3",
+                    "biopython": 1.79
                 },
                 "Workflow": {
                     "nf-core/proteinfold": "v2.1.0dev"
@@ -88,7 +88,8 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
                 "reports",
-                "reports/test_alphafold2_report.html"
+                "reports/T1024_alphafold2_report.html",
+                "reports/T1026_alphafold2_report.html"
             ],
             [
                 "mgy_clusters.fa:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -131,13 +132,14 @@
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "T1024_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
+        "timestamp": "2026-05-29T12:01:54.780944659",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-04-24T10:38:04.23112396"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
diff --git a/tests/alphafold2_split.nf.test.snap b/tests/alphafold2_split.nf.test.snap
@@ -8,18 +8,18 @@
                     "generate_report.py": "Python 3.12.7"
                 },
                 "RUN_ALPHAFOLD2_MSA": {
-                    "python": null,
+                    "python": "3.11.14",
                     "alphafold2": "unknown",
-                    "numpy": "unknown",
-                    "biopython": "unknown"
+                    "numpy": "1.24.3",
+                    "biopython": 1.79
                 },
                 "RUN_ALPHAFOLD2_PRED": {
-                    "python": null,
+                    "python": "3.11.14",
                     "alphafold2": "unknown",
-                    "jax": "unknown",
-                    "jaxlib": "unknown",
-                    "numpy": "unknown",
-                    "biopython": "unknown"
+                    "jax": "0.4.26",
+                    "jaxlib": "0.4.26",
+                    "numpy": "1.24.3",
+                    "biopython": 1.79
                 },
                 "Workflow": {
                     "nf-core/proteinfold": "v2.1.0dev"
@@ -64,7 +64,8 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
                 "reports",
-                "reports/test_alphafold2_report.html"
+                "reports/T1024_alphafold2_report.html",
+                "reports/T1026_alphafold2_report.html"
             ],
             [
                 "T1024_alphafold2_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -89,13 +90,14 @@
                 "T1026.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "T1024_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
+        "timestamp": "2026-05-29T12:02:08.331526798",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-04-24T10:38:24.179333033"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
diff --git a/tests/alphafold3.nf.test.snap b/tests/alphafold3.nf.test.snap
@@ -17,18 +17,18 @@
                     "python": "3.12.7"
                 },
                 "RUN_ALPHAFOLD3_DATAPIPELINE": {
-                    "python": "unknown",
+                    "python": "3.11.12",
                     "alphafold3": "unknown",
-                    "hmmer": "unknown"
+                    "hmmer": 3.4
                 },
                 "RUN_ALPHAFOLD3_INFERENCE": {
-                    "python": "unknown",
+                    "python": "3.11.12",
                     "alphafold3": "unknown",
-                    "jax": "unknown",
-                    "jaxlib": "unknown",
-                    "numpy": "unknown",
-                    "biopython": "unknown",
-                    "rdkit": "unknown"
+                    "jax": "0.4.34",
+                    "jaxlib": "0.4.34",
+                    "numpy": "2.1.3",
+                    "biopython": 1.85,
+                    "rdkit": "2024.03.5"
                 },
                 "Workflow": {
                     "nf-core/proteinfold": "v2.1.0dev"
@@ -86,7 +86,8 @@
                 "pipeline_info",
                 "pipeline_info/nf_core_proteinfold_software_mqc_versions.yml",
                 "reports",
-                "reports/test_alphafold2_report.html"
+                "reports/T1024_alphafold3_report.html",
+                "reports/T1026_alphafold3_report.html"
             ],
             [
                 "T1024_alphafold3_msa.tsv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -125,13 +126,14 @@
                 "T1026_ranked_5.cif.pdb:md5,d41d8cd98f00b204e9800998ecf8427e",
                 ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test_alphafold2_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                "T1024_alphafold3_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "T1026_alphafold3_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
             ]
         ],
+        "timestamp": "2026-05-29T12:02:22.195461228",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.4"
-        },
-        "timestamp": "2026-05-16T00:02:51.199631231"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }