nf-core · jscgh · May 20, 2025 · May 16, 2025 · May 16, 2025 · May 16, 2025
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,10 +4,17 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
+          - prettier@3.5.3
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-added-large-files
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+    rev: "3.2.1"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#235](https://github.com/nf-core/proteinfold/issues/235)] - Update samplesheet to new version (switch from `sequence` column to `id`).
 - [[#239](https://github.com/nf-core/proteinfold/issues/239)] - Update alphafold2 standard mode Dockerfile.
 - [[#240](https://github.com/nf-core/proteinfold/issues/240)] - Separate download and input of pdb `mmcif` files and `obsolete` database.
+- [[#229](https://github.com/nf-core/proteinfold/issues/229)] - Add Boltz pipeline [PR #227](https://github.com/nf-core/proteinfold/pull/227).
 - [[PR #249](https://github.com/nf-core/proteinfold/pull/249)] - Update pipeline template to [nf-core/tools 3.2.0](https://github.com/nf-core/tools/releases/tag/3.2.0).
 - [[PR #271](https://github.com/nf-core/proteinfold/pull/271)] - Update RFAA and HF3 dockerfiles for quicker building and reduction in image size.
 - [[PR #274](https://github.com/nf-core/proteinfold/pull/274)] - Simplify run_helixfold3 module and move arguments to `modules.config`.
@@ -35,8 +36,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#273](https://github.com/nf-core/proteinfold/issues/273)] - Fixes comparison report to correctly label msa coverage plots with corresponding method label.
 - [[#290](https://github.com/nf-core/proteinfold/issues/290)] - Update Alphafold2 split images to make them compatible Hopper gpus.
 - [[PR #302](https://github.com/nf-core/proteinfold/pull/302)] - Fix HF3 dbs and max_template_date.
-- [[#305](https://github.com/nf-core/proteinfold/pull/305)] - Stop RFAA and HF3 symlinking scripts into workdir.
+- [[PR #305](https://github.com/nf-core/proteinfold/pull/305)] - Stop RFAA and HF3 symlinking scripts into workdir.
 - [[PR #306](https://github.com/nf-core/proteinfold/pull/306)] - extract_output.py -> extract_metrics.py so pLDDT, MSA, PAE emitted as raw data .tsv files
+- [[PR #307](https://github.com/nf-core/proteinfold/pull/307)] - Update Boltz-1 boilerplate and formatting.
 
 ### Parameters
 

diff --git a/conf/dbs.config b/conf/dbs.config
@@ -35,6 +35,14 @@ params {
     pdb_seqres_path          = "${params.alphafold2_db}/pdb_seqres/*"
     uniprot_path             = "${params.alphafold2_db}/uniprot/*"
 
+    // Boltz links
+    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_conf.ckpt'
+
+    // Boltz paths
+    boltz_ccd_path           = "${params.boltz_db}/ccd.pkl"
+    boltz_model_path         = "${params.boltz_db}/boltz1_conf.ckpt"
+
     // Colabfold links
     colabfold_db_link       = 'http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz'
     uniref30_colabfold_link = 'https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gz'
@@ -99,13 +107,6 @@ params {
     // Esmfold paths
     esmfold_params_path                  = "${params.esmfold_db}/*"
 
-    // boltz paths
-    boltz_ccd_path                       = "${params.boltz_db}/ccd.pkl"
-    boltz_model_path                     = "${params.boltz_db}/boltz1.ckpt"
-    // boltz links
-    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'
-
     // Foldseek databases paths
     foldseek_db = null
     foldseek_db_path = null

diff --git a/conf/test_colabfold_local.config b/conf/test_colabfold_local.config
@@ -35,4 +35,3 @@ process {
         container = 'biocontainers/gawk:5.1.0'
     }
 }
-
diff --git a/conf/test_esmfold.config b/conf/test_esmfold.config
@@ -34,4 +34,3 @@ process {
         container = 'quay.io/biocontainers/gawk:5.1.0'
     }
 }
-
diff --git a/conf/test_full_boltz.config b/conf/test_full_boltz.config
@@ -9,6 +9,7 @@
 
 ----------------------------------------------------------------------------------------
 */
+
 params {
     config_profile_name        = 'Full test profile for boltz'
     config_profile_description = 'Minimal test dataset to check pipeline function'

diff --git a/conf/test_helixfold3.config b/conf/test_helixfold3.config
@@ -34,4 +34,3 @@ process {
         container = 'biocontainers/gawk:5.1.0'
     }
 }
-
diff --git a/dockerfiles/Dockerfile_nfcore-proteinfold_boltz b/dockerfiles/Dockerfile_nfcore-proteinfold_boltz
@@ -14,5 +14,3 @@ RUN  apt-get update && \
 RUN pip install boltz
 
 CMD ["boltz"]
-
-
diff --git a/modules/local/data_convertor/boltz_fasta/main.nf b/modules/local/data_convertor/boltz_fasta/main.nf
@@ -56,6 +56,7 @@ process BOLTZ_FASTA {
 
     with open ("versions.yml", "w") as version_file:
         version_file.write("\\"${task.process}\\":\\n    python: {}\\n".format(sys.version.split()[0].strip()))
+    ${args}
     """
 
     stub:

diff --git a/modules/local/run_boltz/main.nf b/modules/local/run_boltz/main.nf
@@ -4,10 +4,9 @@
 process RUN_BOLTZ {
     tag "$meta.id"
     label 'process_medium'
-    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
-        error("Local RUN_BOLTZ module does not support Conda. Please use Docker / Singularity / Podman instead.")
-    }
-    container "quay.io/nf-core/proteinfold_boltz:dev"
+    label 'process_gpu'
+
+    container "nf-core/proteinfold_boltz:dev"
 
     input:
     tuple val(meta), path(fasta)
@@ -30,6 +29,10 @@ process RUN_BOLTZ {
     task.ext.when == null || task.ext.when
 
     script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error("Local RUN_BOLTZ module does not support Conda. Please use Docker / Singularity / Podman instead.")
+    }
     def version = "0.4.1"
     def args = task.ext.args ?: ''
 

diff --git a/modules/nf-core/aria2/aria2.diff b/modules/nf-core/aria2/aria2.diff
diff --git a/modules/nf-core/aria2/tests/main.nf.test.snap b/modules/nf-core/aria2/tests/main.nf.test.snap
diff --git a/modules/nf-core/foldseek/easysearch/foldseek-easysearch.diff b/modules/nf-core/foldseek/easysearch/foldseek-easysearch.diff
diff --git a/modules/nf-core/foldseek/easysearch/tests/main.nf.test.snap b/modules/nf-core/foldseek/easysearch/tests/main.nf.test.snap
diff --git a/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap b/modules/nf-core/mmseqs/createindex/tests/main.nf.test.snap
diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap
diff --git a/modules/nf-core/untar/untar.diff b/modules/nf-core/untar/untar.diff
diff --git a/nextflow.config b/nextflow.config
@@ -11,7 +11,7 @@ params {
 
     // Input options
     input                       = null
-    mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, helixfold3}
+    mode                        = 'alphafold2' // {alphafold2, colabfold, esmfold, rosettafold_all_atom, helixfold3, boltz}
     use_gpu                     = false
     split_fasta                 = false
 
@@ -50,6 +50,16 @@ params {
     pdb_seqres_path             = null
     uniprot_path                = null
 
+    // Boltz links
+    boltz_ccd_link           = null
+    boltz_model_link         = null
+
+    // Boltz paths
+    boltz_db                    = null
+    boltz_ccd_path              = null
+    boltz_model_path            = null
+    boltz_use_msa_server        = true
+
     // Colabfold parameters
     colabfold_server            = "webserver"
     colabfold_model_preset      = "alphafold2_ptm" // {'auto', 'alphafold2', 'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'}
@@ -321,6 +331,7 @@ profiles {
     test_full_colabfold_multimer  { includeConfig 'conf/test_full_colabfold_webserver_multimer.config' }
     test_full_esmfold             { includeConfig 'conf/test_full_esmfold.config'                      }
     test_full_esmfold_multimer    { includeConfig 'conf/test_full_esmfold_multimer.config'             }
+    test_full_boltz               { includeConfig 'conf/test_full_boltz.config'                        }
     test_rosettafold_all_atom     { includeConfig 'conf/test_rosettafold_all_atom.config'              }
     test_helixfold3               { includeConfig 'conf/test_helixfold3.config'                        }
     test_full_boltz               { includeConfig 'conf/test_full_boltz.config'                        }
Original file line number	Diff line number	Diff line change
Expand Up		@@ -35,4 +35,3 @@ process {
		container = 'biocontainers/gawk:5.1.0'
		}
		}
Original file line number	Diff line number	Diff line change
Expand Up		@@ -34,4 +34,3 @@ process {
		container = 'quay.io/biocontainers/gawk:5.1.0'
		}
		}
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,6 +9,7 @@ @@
     ----------------------------------------------------------------------------------------
     */
     params {
         config_profile_name        = 'Full test profile for boltz'
         config_profile_description = 'Minimal test dataset to check pipeline function'
@@ Expand Down @@
Original file line number	Diff line number	Diff line change
Expand Up		@@ -14,5 +14,3 @@ RUN apt-get update && \
		RUN pip install boltz

		CMD ["boltz"]