Update for Boltz-2 #329

jscgh · 2025-06-10T07:29:21Z

Updates the Boltz image and adds db paths for Boltz-2.

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
CHANGELOG.md is updated.

…ing/proteinfold into dev

nf-core-bot · 2025-06-10T07:29:53Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2025-06-10T07:30:31Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 8912385

+| ✅ 322 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  76 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
schema_description - Ungrouped param in schema: boltz_output_format
schema_description - No description provided in schema for parameter: random_seed
schema_description - No description provided in schema for parameter: boltz_out_dir
schema_description - No description provided in schema for parameter: boltz_msa_server_url
schema_description - No description provided in schema for parameter: boltz_use_potentials
schema_description - No description provided in schema for parameter: boltz_write_full_pae
schema_description - No description provided in schema for parameter: boltz_model
schema_description - No description provided in schema for parameter: model_name
schema_description - No description provided in schema for parameter: preset
schema_description - No description provided in schema for parameter: init_model
schema_description - No description provided in schema for parameter: logging_level
schema_description - No description provided in schema for parameter: precision
schema_description - No description provided in schema for parameter: infer_times
schema_description - No description provided in schema for parameter: helixfold3_max_template_date
schema_description - No description provided in schema for parameter: boltz2_aff_link
schema_description - No description provided in schema for parameter: boltz2_conf_link
schema_description - No description provided in schema for parameter: boltz2_mols_link
schema_description - No description provided in schema for parameter: boltz2_aff_path
schema_description - No description provided in schema for parameter: boltz2_conf_path
schema_description - No description provided in schema for parameter: boltz2_mols_path
schema_description - No description provided in schema for parameter: uniref30_rosettafold_all_atom_link
schema_description - No description provided in schema for parameter: bfd_rosettafold_all_atom_link
schema_description - No description provided in schema for parameter: pdb100_rosettafold_all_atom_link
schema_description - No description provided in schema for parameter: rfaa_paper_weights_link
schema_description - No description provided in schema for parameter: rosettafold_all_atom_db
schema_description - No description provided in schema for parameter: uniref30_rosettafold_all_atom_path
schema_description - No description provided in schema for parameter: bfd_rosettafold_all_atom_path
schema_description - No description provided in schema for parameter: pdb100_rosettafold_all_atom_path
schema_description - No description provided in schema for parameter: rfaa_paper_weights_path
schema_description - No description provided in schema for parameter: helixfold3_db
schema_description - No description provided in schema for parameter: helixfold3_init_models_path
schema_description - No description provided in schema for parameter: helixfold3_uniclust30_path
schema_description - No description provided in schema for parameter: helixfold3_ccd_preprocessed_path
schema_description - No description provided in schema for parameter: helixfold3_rfam_path
schema_description - No description provided in schema for parameter: helixfold3_bfd_path
schema_description - No description provided in schema for parameter: helixfold3_small_bfd_path
schema_description - No description provided in schema for parameter: helixfold3_uniprot_path
schema_description - No description provided in schema for parameter: helixfold3_pdb_seqres_path
schema_description - No description provided in schema for parameter: helixfold3_uniref90_path
schema_description - No description provided in schema for parameter: helixfold3_mgnify_path
schema_description - No description provided in schema for parameter: helixfold3_pdb_mmcif_path
schema_description - No description provided in schema for parameter: helixfold3_maxit_src_path
schema_description - No description provided in schema for parameter: helixfold3_obsolete_path
schema_description - No description provided in schema for parameter: helixfold3_init_models_link
schema_description - No description provided in schema for parameter: helixfold3_uniclust30_link
schema_description - No description provided in schema for parameter: helixfold3_ccd_preprocessed_link
schema_description - No description provided in schema for parameter: helixfold3_rfam_link
schema_description - No description provided in schema for parameter: helixfold3_bfd_link
schema_description - No description provided in schema for parameter: helixfold3_small_bfd_link
schema_description - No description provided in schema for parameter: helixfold3_pdb_seqres_link
schema_description - No description provided in schema for parameter: helixfold3_uniref90_link
schema_description - No description provided in schema for parameter: helixfold3_mgnify_link
schema_description - No description provided in schema for parameter: helixfold3_pdb_mmcif_link
schema_description - No description provided in schema for parameter: helixfold3_uniprot_sprot_link
schema_description - No description provided in schema for parameter: helixfold3_uniprot_trembl_link
schema_description - No description provided in schema for parameter: helixfold3_pdb_obsolete_link
schema_description - No description provided in schema for parameter: helixfold3_obsolete_link
local_component_structure - prepare_alphafold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_colabfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_esmfold_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_rosettafold_all_atom_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_helixfold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - aria2_uncompress.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_boltz_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - post_processing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_alphafold2_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-proteinfold_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-proteinfold_logo_light.png
files_exist - File found: docs/images/nf-core-proteinfold_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-proteinfold_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowProteinfold.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.2.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.boltz_output_format= pdb
nextflow_config - Config default value correct: params.mode= alphafold2
nextflow_config - Config default value correct: params.uniref30_prefix= UniRef30_2023_02
nextflow_config - Config default value correct: params.max_template_date= 2038-01-19
nextflow_config - Config default value correct: params.alphafold2_mode= standard
nextflow_config - Config default value correct: params.alphafold2_model_preset= monomer
nextflow_config - Config default value correct: params.alphafold2_params_prefix= alphafold_params_2022-12-06
nextflow_config - Config default value correct: params.colabfold_server= webserver
nextflow_config - Config default value correct: params.colabfold_model_preset= alphafold2_ptm
nextflow_config - Config default value correct: params.num_recycles_colabfold= 3
nextflow_config - Config default value correct: params.use_amber= true
nextflow_config - Config default value correct: params.use_templates= true
nextflow_config - Config default value correct: params.num_recycles_esmfold= 4
nextflow_config - Config default value correct: params.esmfold_model_preset= monomer
nextflow_config - Config default value correct: params.boltz_write_full_pae= true
nextflow_config - Config default value correct: params.helixfold3_max_template_date= 2038-01-19
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.bfd_link= https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
nextflow_config - Config default value correct: params.alphafold2_small_bfd_link= https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz
nextflow_config - Config default value correct: params.alphafold2_params_link= https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar
nextflow_config - Config default value correct: params.alphafold2_mgnify_link= https://storage.googleapis.com/alphafold-databases/v2.3/mgy_clusters_2022_05.fa.gz
nextflow_config - Config default value correct: params.pdb70_link= http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200916.tar.gz
nextflow_config - Config default value correct: params.alphafold2_pdb_mmcif_link= rsync.rcsb.org::ftp_data/structures/divided/mmCIF/
nextflow_config - Config default value correct: params.pdb_obsolete_link= https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat
nextflow_config - Config default value correct: params.alphafold2_uniref30_link= https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz
nextflow_config - Config default value correct: params.alphafold2_uniref90_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz
nextflow_config - Config default value correct: params.alphafold2_pdb_seqres_link= https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
nextflow_config - Config default value correct: params.uniprot_sprot_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
nextflow_config - Config default value correct: params.uniprot_trembl_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
nextflow_config - Config default value correct: params.bfd_path= null/bfd/*
nextflow_config - Config default value correct: params.alphafold2_small_bfd_path= null/small_bfd/*
nextflow_config - Config default value correct: params.alphafold2_params_path= null/params/alphafold_params_2022-12-06/*
nextflow_config - Config default value correct: params.alphafold2_mgnify_path= null/mgnify/*
nextflow_config - Config default value correct: params.pdb70_path= null/pdb70/*
nextflow_config - Config default value correct: params.alphafold2_pdb_mmcif_path= null/pdb_mmcif/mmcif_files
nextflow_config - Config default value correct: params.pdb_obsolete_path= null/pdb_mmcif/obsolete.dat
nextflow_config - Config default value correct: params.alphafold2_uniref30_path= null/uniref30/*
nextflow_config - Config default value correct: params.alphafold2_uniref90_path= null/uniref90/*
nextflow_config - Config default value correct: params.alphafold2_pdb_seqres_path= null/pdb_seqres/*
nextflow_config - Config default value correct: params.alphafold2_uniprot_path= null/uniprot/*
nextflow_config - Config default value correct: params.alphafold3_small_bfd_link= https://storage.googleapis.com/alphafold-databases/v3.0/bfd-first_non_consensus_sequences.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_mgnify_link= https://storage.googleapis.com/alphafold-databases/v3.0/mgy_clusters_2022_05.fa.zst
nextflow_config - Config default value correct: params.alphafold3_pdb_mmcif_link= https://storage.googleapis.com/alphafold-databases/v3.0/pdb_2022_09_28_mmcif_files.tar.zst
nextflow_config - Config default value correct: params.alphafold3_uniref90_link= https://storage.googleapis.com/alphafold-databases/v3.0/uniref90_2022_05.fa.zst
nextflow_config - Config default value correct: params.alphafold3_pdb_seqres_link= https://storage.googleapis.com/alphafold-databases/v3.0/pdb_seqres_2022_09_28.fasta.zst
nextflow_config - Config default value correct: params.uniprot_link= https://storage.googleapis.com/alphafold-databases/v3.0/uniprot_all_2021_04.fa.zst
nextflow_config - Config default value correct: params.alphafold3_small_bfd_path= null/small_bfd/*
nextflow_config - Config default value correct: params.alphafold3_params_path= null/params/*
nextflow_config - Config default value correct: params.alphafold3_mgnify_path= null/mgnify/*
nextflow_config - Config default value correct: params.alphafold3_pdb_mmcif_path= null/mmcif_files
nextflow_config - Config default value correct: params.alphafold3_uniref90_path= null/uniref90/*
nextflow_config - Config default value correct: params.alphafold3_pdb_seqres_path= null/pdb_seqres/*
nextflow_config - Config default value correct: params.alphafold3_uniprot_path= null/uniprot/*
nextflow_config - Config default value correct: params.colabfold_db_link= http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz
nextflow_config - Config default value correct: params.colabfold_uniref30_link= https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gz
nextflow_config - Config default value correct: params.colabfold_db_path= null/colabfold_envdb/*
nextflow_config - Config default value correct: params.colabfold_uniref30_path= null/colabfold_uniref30/*
nextflow_config - Config default value correct: params.esmfold_3B_v1= https://dl.fbaipublicfiles.com/fair-esm/models/esmfold_3B_v1.pt
nextflow_config - Config default value correct: params.esm2_t36_3B_UR50D= https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t36_3B_UR50D.pt
nextflow_config - Config default value correct: params.esm2_t36_3B_UR50D_contact_regression= https://dl.fbaipublicfiles.com/fair-esm/regression/esm2_t36_3B_UR50D-contact-regression.pt
nextflow_config - Config default value correct: params.esmfold_params_path= null/params/*
nextflow_config - Config default value correct: params.boltz_ccd_link= https://huggingface.co/boltz-community/boltz-1/resolve/main/ccd.pkl
nextflow_config - Config default value correct: params.boltz_model_link= https://huggingface.co/boltz-community/boltz-1/resolve/main/boltz1_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_aff_link= https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_aff.ckpt
nextflow_config - Config default value correct: params.boltz2_conf_link= https://huggingface.co/boltz-community/boltz-2/resolve/main/boltz2_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_mols_link= https://huggingface.co/boltz-community/boltz-2/resolve/main/mols.tar
nextflow_config - Config default value correct: params.boltz_ccd_path= null/params/ccd.pkl
nextflow_config - Config default value correct: params.boltz_model_path= null/params/boltz1_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_aff_path= null/params/boltz2_aff.ckpt
nextflow_config - Config default value correct: params.boltz2_conf_path= null/params/boltz2_conf.ckpt
nextflow_config - Config default value correct: params.boltz2_mols_path= null/params/mols/
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nextflow_config - Config default value correct: params.uniref30_rosettafold_all_atom_link= http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
nextflow_config - Config default value correct: params.bfd_rosettafold_all_atom_link= https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
nextflow_config - Config default value correct: params.pdb100_rosettafold_all_atom_link= https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
nextflow_config - Config default value correct: params.rfaa_paper_weights_link= http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt
nextflow_config - Config default value correct: params.uniref30_rosettafold_all_atom_path= null/uniref30/*
nextflow_config - Config default value correct: params.bfd_rosettafold_all_atom_path= null/bfd/*
nextflow_config - Config default value correct: params.pdb100_rosettafold_all_atom_path= null/pdb100/*
nextflow_config - Config default value correct: params.rfaa_paper_weights_path= null/params/RFAA_paper_weights.pt
nextflow_config - Config default value correct: params.helixfold3_init_models_path= null/params/HelixFold3-240814.pdparams
nextflow_config - Config default value correct: params.helixfold3_uniclust30_path= null/uniref30/*
nextflow_config - Config default value correct: params.helixfold3_ccd_preprocessed_path= null/params/ccd_preprocessed_etkdg.pkl.gz
nextflow_config - Config default value correct: params.helixfold3_rfam_path= null/rfam/Rfam-14.9_rep_seq.fasta
nextflow_config - Config default value correct: params.helixfold3_bfd_path= null/bfd/*
nextflow_config - Config default value correct: params.helixfold3_small_bfd_path= null/small_bfd/*
nextflow_config - Config default value correct: params.helixfold3_uniprot_path= null/uniprot/*
nextflow_config - Config default value correct: params.helixfold3_pdb_seqres_path= null/pdb_seqres/*
nextflow_config - Config default value correct: params.helixfold3_uniref90_path= null/uniref90/*
nextflow_config - Config default value correct: params.helixfold3_mgnify_path= null/mgnify/*
nextflow_config - Config default value correct: params.helixfold3_pdb_mmcif_path= null/pdb_mmcif/mmcif_files
nextflow_config - Config default value correct: params.helixfold3_maxit_src_path= null/maxit-v11.200-prod-src
nextflow_config - Config default value correct: params.helixfold3_obsolete_path= null/pdb_mmcif/obsolete.dat
nextflow_config - Config default value correct: params.helixfold3_init_models_link= https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip
nextflow_config - Config default value correct: params.helixfold3_uniclust30_link= https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz
nextflow_config - Config default value correct: params.helixfold3_ccd_preprocessed_link= https://paddlehelix.bd.bcebos.com/HelixFold3/CCD/ccd_preprocessed_etkdg.pkl.gz
nextflow_config - Config default value correct: params.helixfold3_rfam_link= https://paddlehelix.bd.bcebos.com/HelixFold3/MSA/Rfam-14.9_rep_seq.fasta
nextflow_config - Config default value correct: params.helixfold3_bfd_link= https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
nextflow_config - Config default value correct: params.helixfold3_small_bfd_link= https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz
nextflow_config - Config default value correct: params.helixfold3_pdb_seqres_link= https://files.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt
nextflow_config - Config default value correct: params.helixfold3_uniref90_link= ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz
nextflow_config - Config default value correct: params.helixfold3_mgnify_link= https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz
nextflow_config - Config default value correct: params.helixfold3_pdb_mmcif_link= rsync.rcsb.org::ftp_data/structures/divided/mmCIF/
nextflow_config - Config default value correct: params.helixfold3_uniprot_sprot_link= ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
nextflow_config - Config default value correct: params.helixfold3_uniprot_trembl_link= ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
nextflow_config - Config default value correct: params.helixfold3_obsolete_link= https://files.rcsb.org/pub/pdb/data/status/obsolete.dat
nf_test_content - 'tests/alphafold2_split.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold2_split.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold2_split.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_webserver.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_webserver.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_webserver.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold2_download.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold2_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold2_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/split_fasta.nf.test' contains outdir parameter
nf_test_content - 'tests/split_fasta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/split_fasta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_download.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_local.nf.test' contains outdir parameter
nf_test_content - 'tests/colabfold_local.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/colabfold_local.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold3.nf.test' contains outdir parameter
nf_test_content - 'tests/alphafold3.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/alphafold3.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/esmfold.nf.test' contains outdir parameter
nf_test_content - 'tests/esmfold.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/esmfold.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-proteinfold_logo_light.png matches the template
files_unchanged - docs/images/nf-core-proteinfold_logo_light.png matches the template
files_unchanged - docs/images/nf-core-proteinfold_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
modules_config - ARIA2 found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - FOLDSEEK_EASYSEARCH found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.1
Run at 2025-07-29 06:46:02

modules/local/data_convertor/boltz_fasta/main.nf

main.nf

tlitfin-unsw · 2025-06-17T09:06:23Z

Boltz-1 will be supported after this PR in boltz repo.

jscgh · 2025-07-07T00:22:54Z

Boltz-1 will be supported after this PR in boltz repo.

This PR has now been merged into the Boltz repo.

JoseEspinosa

Nice job! 😄
I have some questions though

conf/modules_boltz.config

conf/dbs.config

main.nf

nextflow.config

nextflow_schema.json

subworkflows/local/prepare_boltz_dbs.nf

Adds consistency to boltz variable names Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

jscgh · 2025-07-29T06:54:01Z

Nice job! 😄 I have some questions though

Thank you, good suggestions!

JoseEspinosa

Thank you! 😄

jscgh added 20 commits May 16, 2025 10:00

Adds process_gpu label

004ba76

Formatting

72e569b

Merge remote-tracking branch 'upstream/dev' into process_gpu

9d615fe

Merge remote-tracking branch 'upstream/dev' into dev

d830605

Fix typo

dad9ad6

Merge branch 'dev' of github.com:Australian-Structural-Biology-Comput…

20333e6

…ing/proteinfold into dev

Update boltz dockerfile

239d5ee

Update container

5457f69

Linted

e033d1a

Update python for boltz-2 compatibility

6f944ec

Build-essentials

9e55ad3

Update boltz

a9478f2

boltz

3ff9bae

Update boltz to include boltz-2

98c8514

Linted

07ed19a

Organised schema

c09565b

Updated boltz and mols pathing

e15fc54

Remove repeated boltz flags and fix caching

1e66273

Moved env variables to run_boltz

0341b90

Fix boltz_fasta preprocessing

c377695

Update changelog, fix container

7d94536

tlitfin-unsw reviewed Jun 10, 2025

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tlitfin-unsw reviewed Jun 10, 2025

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main.nf Outdated Show resolved Hide resolved

Add boltz args and improve matching for entity type

de4b5b3

jscgh force-pushed the boltz-dockerfile branch from b5707d0 to de4b5b3 Compare June 11, 2025 01:51

jscgh added 2 commits June 11, 2025 11:54

Fix escaped char

732c32a

Added missing --boltz_model

3638472

jscgh linked an issue Jun 17, 2025 that may be closed by this pull request

boltz_fasta relabels all inputs as |protein #326

Closed

tlitfin-unsw marked this pull request as draft June 17, 2025 09:04

Merge branch 'dev' into boltz-dockerfile

ae4a887

jscgh marked this pull request as ready for review July 7, 2025 00:36

jscgh added 5 commits July 8, 2025 15:00

Fixed unmatched parenthesis

542d806

Add dna and rna to boltz entities

be68201

Removed unneeded boltz params

593cc3e

Merge remote-tracking branch 'upstream/dev' into boltz-dockerfile

9217904

Added back boltz_output_format with pdb default

b27f09d

JoseEspinosa requested changes Jul 28, 2025

View reviewed changes

jscgh and others added 5 commits July 29, 2025 10:57

Apply suggestions from code review

30e2032

Adds consistency to boltz variable names Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

Updated changelog with parameters

4887c7f

Updated prepare_boltz_dbs

eb04374

Merge remote-tracking branch 'upstream/dev' into boltz-dockerfile

ceb8085

Added boltz_db to prepare_boltz_dbs

8912385

jscgh requested a review from JoseEspinosa July 29, 2025 06:54

JoseEspinosa approved these changes Jul 29, 2025

View reviewed changes

JoseEspinosa merged commit 9d8e8e3 into nf-core:dev Jul 29, 2025
20 checks passed

JoseEspinosa mentioned this pull request Jul 29, 2025

Add multimer confidence metrics (i)pTM to extraction #312

Merged

5 tasks

jscgh deleted the boltz-dockerfile branch July 30, 2025 00:08

jscgh mentioned this pull request Jul 31, 2025

boltz_fasta relabels all inputs as |protein #326

Closed

jscgh mentioned this pull request Aug 20, 2025

Merge upstream dev (2.0.0rc1) Australian-Structural-Biology-Computing/proteinfold#19

Merged

Update for Boltz-2 #329

Update for Boltz-2 #329

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jscgh commented Jun 10, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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tlitfin-unsw commented Jun 17, 2025

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nf-core-bot commented Jun 10, 2025 •

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️