Merge pull request #356 from tlitfin-unsw/change-af2-defaults

jscgh · web-flow · commit 38aff42d9189 · 2025-08-06T17:23:25.000+10:00
Update AF2 defaults
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -53,6 +53,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #346](https://github.com/nf-core/proteinfold/pull/346)] - Update pipeline template to [nf-core/tools 3.3.2](https://github.com/nf-core/tools/releases/tag/3.3.2).
 - [[PR #351](https://github.com/nf-core/proteinfold/pull/351)] - add chain-wise (i)pTM values and summary file for AF3-generation codes.
 - [[PR #355](https://github.com/nf-core/proteinfold/pull/355)] - Remove unneccesary params from Boltz and Helixfold3 modes.
+- [[PR #356](https://github.com/nf-core/proteinfold/pull/356)] - Update AF2 defaults to use split mode and monomer_ptm model.
 - [[PR #360](https://github.com/nf-core/proteinfold/pull/360)] - Rename some DBs paths in the run modules so they are equal to those when DBs are downloaded.
 - [[PR #362](https://github.com/nf-core/proteinfold/pull/355)] - Update boltz Dockerfile and image pinging specific version (2.0.3).
 
diff --git a/conf/modules.config b/conf/modules.config
@@ -30,7 +30,7 @@ process {
     withName: 'UNTAR' {
         ext.args2 = '--no-same-owner'
         publishDir = [
-            path: {"${params.outdir}/DBs/${params.mode}/${params.alphafold2_mode}"},
+            path: {"${params.outdir}/DBs/${params.mode}"},
             mode: 'symlink',
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
diff --git a/conf/modules_alphafold2.config b/conf/modules_alphafold2.config
@@ -17,7 +17,7 @@
 process {
     withName: 'GUNZIP|COMBINE_UNIPROT|DOWNLOAD_PDBMMCIF|ARIA2_PDB_SEQRES' {
         publishDir = [
-            path: {"${params.outdir}/DBs/alphafold2/${params.alphafold2_mode}"},
+            path: {"${params.outdir}/DBs/alphafold2"},
             mode: 'symlink',
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
diff --git a/nextflow.config b/nextflow.config
@@ -11,16 +11,16 @@ params {
 
     // Input options
     input                       = null
-    mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, helixfold3, boltz}
+    mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, alphafold3, helixfold3, boltz}
     use_gpu                     = false
     split_fasta                 = false
     db                          = null
 
     // Alphafold2 parameters
-    alphafold2_mode             = "standard"
-    max_template_date           = "2038-01-19"
+    alphafold2_mode             = 'split_msa_prediction' // {standard, split_msa_prediction}
+    max_template_date           = '2038-01-19'
     full_dbs                    = false // true full_dbs, false reduced_dbs
-    alphafold2_model_preset     = "monomer" // for AF2 {monomer (default), monomer_casp14, monomer_ptm, multimer}
+    alphafold2_model_preset     = 'monomer_ptm' // for AF2 {monomer, monomer_casp14, monomer_ptm, multimer}
     alphafold2_db               = null
     random_seed                 = null
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -100,14 +100,14 @@
                 },
                 "alphafold2_mode": {
                     "type": "string",
-                    "default": "standard",
+                    "default": "split_msa_prediction",
                     "description": "Specifies the mode in which AlphaFold2 will be run",
                     "enum": ["standard", "split_msa_prediction"],
                     "fa_icon": "fas fa-exchange-alt"
                 },
                 "alphafold2_model_preset": {
                     "type": "string",
-                    "default": "monomer",
+                    "default": "monomer_ptm",
                     "description": "Model preset for 'AlphaFold2' mode",
                     "enum": ["monomer", "monomer_casp14", "monomer_ptm", "multimer"],
                     "fa_icon": "fas fa-stream"
diff --git a/tests/alphafold2_download.nf.test.snap b/tests/alphafold2_download.nf.test.snap
@@ -22,19 +22,18 @@
             [
                 "DBs",
                 "DBs/alphafold2",
-                "DBs/alphafold2/standard",
-                "DBs/alphafold2/standard/UniRef30_2023_02_hhsuite",
-                "DBs/alphafold2/standard/alphafold_params_2022-12-06",
-                "DBs/alphafold2/standard/bfd-first_non_consensus_sequences.fasta",
-                "DBs/alphafold2/standard/mgy_clusters.fa",
-                "DBs/alphafold2/standard/mmcif_files",
-                "DBs/alphafold2/standard/obsolete.dat",
-                "DBs/alphafold2/standard/pdb70_from_mmcif_220313",
-                "DBs/alphafold2/standard/pdb_seqres.txt",
-                "DBs/alphafold2/standard/uniprot.fasta",
-                "DBs/alphafold2/standard/uniprot_sprot.fasta",
-                "DBs/alphafold2/standard/uniprot_trembl.fasta",
-                "DBs/alphafold2/standard/uniref90.fasta",
+                "DBs/alphafold2/UniRef30_2023_02_hhsuite",
+                "DBs/alphafold2/alphafold_params_2022-12-06",
+                "DBs/alphafold2/bfd-first_non_consensus_sequences.fasta",
+                "DBs/alphafold2/mgy_clusters.fa",
+                "DBs/alphafold2/mmcif_files",
+                "DBs/alphafold2/obsolete.dat",
+                "DBs/alphafold2/pdb70_from_mmcif_220313",
+                "DBs/alphafold2/pdb_seqres.txt",
+                "DBs/alphafold2/uniprot.fasta",
+                "DBs/alphafold2/uniprot_sprot.fasta",
+                "DBs/alphafold2/uniprot_trembl.fasta",
+                "DBs/alphafold2/uniref90.fasta",
                 "multiqc",
                 "multiqc/alphafold2_multiqc_data",
                 "multiqc/alphafold2_multiqc_plots",
@@ -70,6 +69,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-08-05T11:15:15.449397416"
+        "timestamp": "2025-08-06T17:07:06.871556244"
     }
 }
diff --git a/tests/colabfold_download.nf.test.snap b/tests/colabfold_download.nf.test.snap
@@ -20,8 +20,7 @@
             [
                 "DBs",
                 "DBs/colabfold",
-                "DBs/colabfold/standard",
-                "DBs/colabfold/standard/alphafold_params_2021-07-14",
+                "DBs/colabfold/alphafold_params_2021-07-14",
                 "colabfold",
                 "colabfold/webserver",
                 "colabfold/webserver/T1024_colabfold.pdb",
@@ -71,8 +70,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-07-24T16:54:46.721482885"
+        "timestamp": "2025-08-04T13:16:31.355330962"
     }
 }
diff --git a/tests/split_fasta.nf.test.snap b/tests/split_fasta.nf.test.snap
@@ -64,8 +64,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-07-24T16:55:26.47855323"
+        "timestamp": "2025-08-04T13:24:37.804124192"
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,7 @@ process {`
`30`	`30`	`withName: 'UNTAR' {`
`31`	`31`	`ext.args2 = '--no-same-owner'`
`32`	`32`	`publishDir = [`
`33`		`- path: {"${params.outdir}/DBs/${params.mode}/${params.alphafold2_mode}"},`
	`33`	`+ path: {"${params.outdir}/DBs/${params.mode}"},`
`34`	`34`	`mode: 'symlink',`
`35`	`35`	`saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`36`	`36`	`]`
Original file line number	Diff line number	Diff line change
`@@ -17,7 +17,7 @@`
`17`	`17`	`process {`
`18`	`18`	`withName: 'GUNZIP\|COMBINE_UNIPROT\|DOWNLOAD_PDBMMCIF\|ARIA2_PDB_SEQRES' {`
`19`	`19`	`publishDir = [`
`20`		`- path: {"${params.outdir}/DBs/alphafold2/${params.alphafold2_mode}"},`
	`20`	`+ path: {"${params.outdir}/DBs/alphafold2"},`
`21`	`21`	`mode: 'symlink',`
`22`	`22`	`saveAs: { filename -> filename.equals('versions.yml') ? null : filename },`
`23`	`23`	`]`
Original file line number	Diff line number	Diff line change
`@@ -64,8 +64,8 @@`
`64`	`64`	`],`
`65`	`65`	`"meta": {`
`66`	`66`	`"nf-test": "0.9.2",`
`67`		`- "nextflow": "24.10.5"`
	`67`	`+ "nextflow": "25.04.6"`
`68`	`68`	`},`
`69`		`- "timestamp": "2025-07-24T16:55:26.47855323"`
	`69`	`+ "timestamp": "2025-08-04T13:24:37.804124192"`
`70`	`70`	`}`
`71`	`71`	`}`