Add Boltz

CHANGELOG.md

@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.
 - [[PR #210](https://github.com/nf-core/proteinfold/pull/210)]- Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure.
 - [[#214](https://github.com/nf-core/proteinfold/issues/214)]- Fix colabfold image to run in cpus after [#188](https://github.com/nf-core/proteinfold/issues/188) fix.
+- [[#229](https://github.com/nf-core/proteinfold/issues/229)]- Add Boltz pipeline [PR #230](https://github.com/nf-core/proteinfold/pull/230).
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
 

conf/dbs.config

@@ -21,6 +21,8 @@ params {
     pdb_seqres_link          = 'https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt'
     uniprot_sprot_link       = 'https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz'
     uniprot_trembl_link      = 'https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz'
+    boltz_ccd_link           = 'https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl'
+    boltz_model_link         = 'https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1.ckpt'
 
     // Alphafold paths
     bfd_path                 = "${params.alphafold2_db}/bfd/*"

main.nf

@@ -27,6 +27,10 @@ if (params.mode.toLowerCase().split(",").contains("esmfold")) {
     include { PREPARE_ESMFOLD_DBS } from './subworkflows/local/prepare_esmfold_dbs'
     include { ESMFOLD             } from './workflows/esmfold'
 }
+if (params.mode.toLowerCase().split(",").contains("boltz")) {
+    include { PREPARE_BOLTZ_DBS } from './subworkflows/local/prepare_boltz_dbs'
+    include { BOLTZ } from './workflows/boltz'
+}
 
 include { PIPELINE_INITIALISATION          } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
 include { PIPELINE_COMPLETION              } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
@@ -205,6 +209,37 @@ workflow NFCORE_PROTEINFOLD {
         ch_report_input           = ch_report_input.mix(ESMFOLD.out.pdb_msa)
     }
 
+    //
+    // WORKFLOW: Run Boltz
+    //
+    if (params.mode.toLowerCase().split(",").contains("boltz")) {
+        PREPARE_BOLTZ_DBS(
+            params.boltz_ccd_path,
+            params.boltz_model_path,
+            params.boltz_ccd_link,
+            params.boltz_model_link
+        )
+        ch_versions = ch_versions.mix(PREPARE_BOLTZ_DBS.out.versions)
+
+        BOLTZ(
+            ch_samplesheet,
+            ch_versions,
+            PREPARE_BOLTZ_DBS.out.boltz_ccd,
+            PREPARE_BOLTZ_DBS.out.boltz_model
+        )
+        ch_versions = ch_versions.mix(BOLTZ.out.versions)
+        ch_report_input = ch_report_input.mix(
+            BOLTZ
+                .out
+                .msa
+                .join(BOLTZ.out.structures)
+                .join(BOLTZ.out.confidence)
+                .join(BOLTZ.out.plddt)
+                .map { it[0]["model"] = "boltz"; it }
+        )
+
+    }
+
     //
     // POST PROCESSING: generate visualisation reports
     //

nextflow.config

@@ -47,6 +47,14 @@ params {
     uniref90_path               = null
     pdb_seqres_path             = null
     uniprot_path                = null
+
+	// Boltz links
+    boltz_ccd_link           = null
+    boltz_model_link         = null
+
+	// Boltz parameters
+    boltz_ccd_path              = null
+    boltz_model_path            = null
 
     // Colabfold parameters
     colabfold_server            = "webserver"

nextflow_schema.json

@@ -296,6 +296,35 @@
                 }
             }
         },
+        "boltz_options": {
+            "title": "Boltz DBs and model paths options",
+            "type": "object",
+            "fa_icon": "fas fa-database",
+            "description": "Paths used to provide model paths and weight paths to Boltz",
+
+            "properties": {
+                "boltz_ccd_link": {
+                    "type": "string",
+                    "description": "Link to download CCD file",
+                    "icon": "fas fa-link"
+                },
+                "boltz_model_link": {
+                    "type": "string",
+                    "description": "Link to download model file",
+                    "icon": "fas fa-link"
+                },
+                "boltz_ccd_path": {
+                    "type": "string",
+                    "description": "Path to CCD path",
+                    "icon": "fas folder-open"
+                },
+                "boltz_model_path": {
+                    "type": "string",
+                    "description": "Path to Model path",
+                    "icon": "fas folder-open"
+                }
+            }
+        },
         "alphafold2_dbs_and_parameters_link_options": {
             "title": "Alphafold2 DBs and parameters links options",
             "type": "object",