Add HelixFold3

.github/CONTRIBUTING.md

@@ -29,7 +29,7 @@ If you're not used to this workflow with git, you can start with some [docs from
 You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
 
 ```bash
-nextflow run . --profile debug,test,docker --outdir <OUTDIR>
+nextflow run . -profile debug,test,docker --outdir <OUTDIR>
 ```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
@@ -78,8 +78,8 @@ If you wish to contribute a new step, please use the following coding standards:
 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool).
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
-8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+8. If applicable, add a new test command in `.github/workflows/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values

.github/workflows/ci.yml

@@ -44,6 +44,7 @@ jobs:
           - "test_colabfold_download"
           - "test_esmfold"
           - "test_split_fasta"
+          - "test_helixfold3"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev

CHANGELOG.md

@@ -15,6 +15,8 @@ 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.
+- [[PR ##220](https://github.com/nf-core/proteinfold/pull/220)] - Add RoseTTAFold-All-Atom module.
+- [[PR ##223](https://github.com/nf-core/proteinfold/pull/223)] - Add HelixFold3 module.
 - [[#235](https://github.com/nf-core/proteinfold/issues/235)] - Update samplesheet to new version (switch from `sequence` column to `id`).
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
@@ -106,6 +108,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 |                       | `--esm2_t36_3B_UR50D_contact_regression` |
 |                       | `--esmfold_params_path`                  |
 |                       | `--skip_multiqc`                         |
+|                       | `--rosettafold_all_atom_db`              |
+|                       | `--helixfold3_db`                        |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.

README.md

@@ -39,6 +39,10 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
    v. [ESMFold](https://github.com/facebookresearch/esm) - Regular ESM
 
+   vi. [RoseTTAFold-All-Atom](https://github.com/baker-laboratory/RoseTTAFold-All-Atom/) - Regular RFAA
+
+   vii. [HelixFold3](https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3) - Regular HF3
+
 ## Usage
 
 > [!NOTE]
@@ -53,7 +57,7 @@ nextflow run nf-core/proteinfold \
    --outdir <OUTDIR>
 ```
 
-The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]. Please refer to the [usage documentation](https://nf-co.re/proteinfold/usage) to check the directory structure you need to provide for each of the databases.
+The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`], [`--esmfold_db`] or ['--rosettafold_all_atom_db']. Please refer to the [usage documentation](https://nf-co.re/proteinfold/usage) to check the directory structure you need to provide for each of the databases.
 
 - The typical command to run AlphaFold2 mode is shown below:
 
@@ -136,6 +140,30 @@ The pipeline takes care of downloading the databases and parameters required by
       -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
   ```
 
+- The rosettafold_all_atom mode can be run using the command below:
+
+  ```console
+  nextflow run nf-core/proteinfold \
+      --input samplesheet.csv \
+      --outdir <OUTDIR> \
+      --mode rosettafold_all_atom \
+      --rosettafold_all_atom_db <null (default) | PATH> \
+      --use_gpu <true/false> \
+      -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+  ```
+
+- The helixfold3 mode can be run using the command below:
+
+  ```console
+  nextflow run nf-core/proteinfold \
+      --input samplesheet.csv \
+      --outdir <OUTDIR> \
+      --mode helixfold3 \
+      --helixfold3_db <null (default) | PATH> \
+      --use_gpu <true/false> \
+      -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+  ```
+
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 

assets/schema_input.json

@@ -7,6 +7,12 @@
     "items": {
         "type": "object",
         "properties": {
+            "sequence": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Sequence name must be provided and cannot contain spaces",
+                "meta": ["sequence"]
+            },
             "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
@@ -17,10 +23,11 @@
                 "type": "string",
                 "format": "file-path",
                 "exists": true,
-                "pattern": "^\\S+\\.fa(sta)?$",
-                "errorMessage": "Fasta file must be provided, cannot contain spaces and must have extension '.fa' or '.fasta'"
+                "pattern": "^\\S+\\.(fa(sta)?|yaml|yml|json)$",
+                "errorMessage": "Fasta, yaml or json file must be provided, cannot contain spaces and must have extension '.fa', '.fasta', '.yaml', '.yml', or '.json'"
             }
         },
-        "required": ["id", "fasta"]
+        "required": ["fasta"],
+        "anyOf": [{ "required": ["sequence"] }, { "required": ["id"] }]
     }
 }

bin/generate_report.py

@@ -307,6 +307,7 @@ def pdb_to_lddt(pdb_files, generate_tsv):
     "esmfold": "ESMFold",
     "alphafold2": "AlphaFold2",
     "colabfold": "ColabFold",
+    "helixfold3": "HelixFold3",
 }
 
 parser = argparse.ArgumentParser()

conf/dbs.config

@@ -48,6 +48,35 @@ params {
         "alphafold2_ptm"         : "alphafold_params_2021-07-14"
     ]
 
+    // Helixfold3 links
+    helixfold3_uniclust30_link          = 'https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz'
+    helixfold3_ccd_preprocessed_link    = 'https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz'
+    helixfold3_rfam_link                = 'https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta'
+    helixfold3_init_models_link         = 'https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip'
+    helixfold3_bfd_link                 = 'https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz'
+    helixfold3_small_bfd_link           = 'https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz'
+    helixfold3_uniprot_sprot_link       = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz'
+    helixfold3_uniprot_trembl_link      = 'ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz'
+    helixfold3_pdb_seqres_link          = "${params.pdb_seqres_link}"
+    helixfold3_uniref90_link            = 'ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz'
+    helixfold3_mgnify_link              = 'https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz'
+    helixfold3_pdb_mmcif_link           = 'rsync.rcsb.org::ftp_data/structures/divided/mmCIF/'
+    helixfold3_pdb_obsolete_link        = 'ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat'
+
+    // Helixfold3 paths
+    helixfold3_uniclust30_path          = "${params.helixfold3_db}/uniclust30/*"
+    helixfold3_ccd_preprocessed_path    = "${params.helixfold3_db}/ccd_preprocessed_etkdg.pkl.gz"
+    helixfold3_rfam_path                = "${params.helixfold3_db}/Rfam-14.9_rep_seq.fasta"
+    helixfold3_init_models_path         = "${params.helixfold3_db}/HelixFold3-240814.pdparams"
+    helixfold3_bfd_path                 = "${params.helixfold3_db}/bfd/*"
+    helixfold3_small_bfd_path           = "${params.helixfold3_db}/small_bfd/*"
+    helixfold3_uniprot_path             = "${params.helixfold3_db}/uniprot/*"
+    helixfold3_pdb_seqres_path          = "${params.helixfold3_db}/pdb_seqres/*"
+    helixfold3_uniref90_path            = "${params.helixfold3_db}/uniref90/*"
+    helixfold3_mgnify_path              = "${params.helixfold3_db}/mgnify/*"
+    helixfold3_pdb_mmcif_path           = "${params.helixfold3_db}/pdb_mmcif/*"
+    helixfold3_maxit_src_path           = "${params.helixfold3_db}/maxit-v11.200-prod-src"
+
     // Esmfold links
     esmfold_3B_v1                        = 'https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt'
     esm2_t36_3B_UR50D                    = 'https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt'

conf/modules_helixfold3.config

@@ -0,0 +1,22 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+process {
+    withName: 'NFCORE_PROTEINFOLD:HELIXFOLD3:MULTIQC' {
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: 'copy',
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "helixfold3_$filename" }
+        ]
+    }
+
+}

conf/test_helixfold3.config

@@ -0,0 +1,37 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+    Use as follows:
+        nextflow run nf-core/proteinfold -profile test_helixfold3,<docker/singularity> --outdir <OUTDIR>
+----------------------------------------------------------------------------------------
+*/
+
+stubRun = true
+
+// Limit resources so that this can run on GitHub Actions
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '15.GB',
+        time: '1.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Input data to test helixfold3
+    mode             = 'helixfold3'
+    helixfold3_db       = "${projectDir}/assets/dummy_db_dir"
+    input            = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv'
+}
+
+process {
+    withName: 'RUN_HELIXFOLD3' {
+        container = '/srv/scratch/sbf-pipelines/proteinfold/singularity/helixfold3.sif'
+    }
+}
+

dockerfiles/Dockerfile_nfcore-proteinfold_helixfold3

@@ -0,0 +1,34 @@
+FROM nvidia/cuda:12.1.1-cudnn8-devel-ubuntu22.04
+
+LABEL Author="[email protected]" \
+    title="nfcore/proteinfold_helixfold3" \
+    Version="0.9.0" \
+    description="Docker image containing all software requirements to run the RUN_HELIXFOLD3 module using the nf-core/proteinfold pipeline"
+
+ENV PYTHONPATH="/app/helixfold3:$PYTHONPATH" \
+    PATH="/conda/bin:/app/helixfold3:$PATH" \
+    PYTHON_BIN="/conda/envs/helixfold/bin/python3.9" \
+    ENV_BIN="/conda/envs/helixfold/bin" \
+    OBABEL_BIN="/conda/envs/helixfold/bin"
+
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y wget git && \
+    wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \
+    bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda && \
+    rm -rf /tmp/Miniforge3-$(uname)-$(uname -m).sh /var/lib/apt/lists/* && \
+    apt-get autoremove -y && apt-get clean -y
+
+RUN git clone --single-branch --branch dev --depth 1 --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git /app/helixfold3 && \
+    cd /app/helixfold3 && \
+    git sparse-checkout init --cone && \
+    git sparse-checkout set apps/protein_folding/helixfold3 && \
+    git checkout dev && \
+    mv apps/protein_folding/helixfold3/* . && \
+    rm -rf apps
+
+COPY hf3_environment.yaml /app/helixfold3/
+RUN /conda/bin/mamba env create --file=/app/helixfold3/hf3_environment.yaml && \
+    /conda/bin/mamba install -y -c bioconda aria2 hmmer==3.3.2 kalign2==2.04 hhsuite==3.3.0 -n helixfold && \
+    /conda/bin/mamba install -y -c conda-forge openbabel -n helixfold && \
+    /conda/bin/mamba clean --all --force-pkgs-dirs -y && \
+    rm -rf /root/.cache && \
+    apt-get autoremove -y && apt-get remove --purge -y wget git && apt-get clean -y

dockerfiles/helixfold3.def

@@ -0,0 +1,48 @@
+Bootstrap: docker
+From: nvidia/cuda:12.6.0-cudnn-devel-ubuntu24.04
+
+%labels
+    Author [email protected]
+    Version 0.2.1
+
+%files
+    environment.yaml .
+
+%post
+    apt update && DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y wget git
+
+    wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
+    bash Miniforge3-Linux-x86_64.sh -b -p /opt/miniforge
+    rm Miniforge3-Linux-x86_64.sh
+    export PATH="/opt/miniforge/bin:$PATH"
+
+    git clone --single-branch --branch dev --depth 1 --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git app/helixfold3
+    cd app/helixfold3
+    git sparse-checkout init --cone
+    git sparse-checkout set apps/protein_folding/helixfold3
+    git checkout dev
+    mv apps/protein_folding/helixfold3/* .
+    rm -rf apps
+    mv /environment.yaml .
+    mamba env create -f environment.yaml
+
+    conda install -y -c bioconda aria2 hmmer==3.3.2 kalign2==2.04 hhsuite==3.3.0 -n helixfold
+    conda install -y -c conda-forge openbabel -n helixfold
+
+    mamba run -n helixfold \
+        'python3 -m pip install paddlepaddle-gpu==2.6.1 -f https://www.paddlepaddle.org.cn/whl/linux/mkl/avx/stable.html && \
+        python3 -m pip install -r requirements.txt'
+
+    apt autoremove -y && apt remove --purge -y wget git && apt clean -y
+    rm -rf /var/lib/apt/lists/* /root/.cache *.tar.gz
+    mamba clean --all --force-pkgs-dirs -y
+
+%environment
+    export PATH="/app/helixfold3:/opt/miniforge/bin:$PATH"
+    export PYTHONPATH="/app/helixfold3:$PYTHONPATH"
+    export PYTHON_BIN="/opt/miniforge/envs/helixfold/bin/python3.9"
+    export ENV_BIN="/opt/miniforge/envs/helixfold/bin"
+    export OBABEL_BIN="/opt/miniforge/envs/helixfold/bin"
+
+%runscript
+    mamba run --name helixfold "$@"

dockerfiles/hf3_environment.yaml

@@ -0,0 +1,35 @@
+name: helixfold
+channels:
+  - conda-forge
+  - bioconda
+  - nvidia
+  - biocore
+
+dependencies:
+  - python=3.9
+  - cuda-toolkit=12.0
+  - cudnn=8.4.0
+  - nccl=2.14
+  - libgcc
+  - libgomp
+  - pip
+  - aria2
+  - hmmer==3.4
+  - kalign2==2.04
+  - hhsuite==3.3.0
+  - openbabel
+  - pip:
+      - paddlepaddle-gpu==2.6.1 -f https://www.paddlepaddle.org.cn/whl/linux/mkl/avx/stable.html
+      - absl-py==0.13.0
+      - biopython==1.79
+      - chex==0.0.7
+      - dm-haiku==0.0.4
+      - dm-tree==0.1.6
+      - docker==5.0.0
+      - immutabledict==2.0.0
+      - jax==0.2.14
+      - ml-collections==0.1.0
+      - pandas==1.3.4
+      - scipy==1.9.0
+      - rdkit-pypi==2022.9.5
+      - posebusters

docs/output.md

@@ -13,6 +13,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and predicts pr
 - [AlphaFold2](https://github.com/deepmind/alphafold)
 - [ColabFold](https://github.com/sokrypton/ColabFold) - MMseqs2 (API server or local search) followed by ColabFold
 - [ESMFold](https://github.com/facebookresearch/esm)
+- [RoseTTAFold-All-Atom](https://github.com/baker-laboratory/RoseTTAFold-All-Atom/)
+- [HelixFold3](https://github.com/PaddlePaddle/PaddleHelix/tree/dev/apps/protein_folding/helixfold3)
 
 See main [README.md](https://github.com/nf-core/proteinfold/blob/master/README.md) for a condensed overview of the steps in the pipeline, and the bioinformatics tools used at each step.
 
@@ -176,6 +178,18 @@ Below you can find an indicative example of the TSV file with the pLDDT scores p
 | 49                 | CB        | VAL          | 7                       | 52.74 |
 | 50                 | O         | VAL          | 7                       | 56.46 |
 
+### HelixFold3
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `run/`
+  - `<SEQUENCE NAME>_helixfold3.pdb` that is the structure with the highest pLDDT score (ranked first)
+  - `<SEQUENCE NAME>_plddt_mqc.tsv` that presents the pLDDT scores per residue for the predicted model
+  - `<SEQUENCE NAME>/` that contains the computed MSAs, prediction metadata, ranked structures, raw model outputs etc.
+
+</details>
+
 ### MultiQC report
 
 <details markdown="1">

docs/usage.md

@@ -426,6 +426,18 @@ If you specify the `--esmfold_db <PATH>` parameter, the directory structure of y
     └── esmfold_3B_v1.pt
 ```
 
+HelixFold3 can be run using this command (note that HF3 requires .json files not .fasta):
+
+```console
+nextflow run nf-core/proteinfold \
+      --input samplesheet.csv \
+      --outdir <OUTDIR> \
+      --mode helixfold3 \
+      --helixfold3_db <null (default) | DB_PATH> \
+      --use_gpu <true/false> \
+      -profile <docker>
+```
+
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
 
 Note that the pipeline will create the following files in your working directory: