Split extract metrics for HelixFold3 by jscgh · Pull Request #566 · nf-core/proteinfold

jscgh · 2026-03-18T07:20:13Z

Splits EXTRACT_METRICS from the HelixFold3 module.
Closes #548

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.

…nfold pipiline

Included meta.yml file for the run_boltz module of the nf-core/protei…

Included meta.yml file for run_alphafold2 module

Split extract_metrics for AlphaFold2

github-actions · 2026-03-18T07:22:01Z

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

Posted for pipeline commit e1735c4

+| ✅ 341 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  32 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
nextflow_config - Config manifest.version should end in dev: 2.0.0
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 nextflow.config: Specify any additional parameters here
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!
schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_link
schema_description - No description provided in schema for parameter: rosettafold2na_bfd_link
schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_link
schema_description - No description provided in schema for parameter: rosettafold2na_weights_link
schema_description - No description provided in schema for parameter: rfam_full_region_link
schema_description - No description provided in schema for parameter: rfam_cm_link
schema_description - No description provided in schema for parameter: rnacentral_rfam_annotations_link
schema_description - No description provided in schema for parameter: rnacentral_id_mapping_link
schema_description - No description provided in schema for parameter: rnacentral_sequences_link
schema_description - No description provided in schema for parameter: rosettafold2na_uniref30_path
schema_description - No description provided in schema for parameter: rosettafold2na_bfd_path
schema_description - No description provided in schema for parameter: rosettafold2na_pdb100_path
schema_description - No description provided in schema for parameter: rosettafold2na_weights_path
local_component_structure - prepare_esmfold_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 - prepare_alphafold3_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_rosettafold2na_dbs.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
local_component_structure - post_processing.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_rosettafold_all_atom_dbs.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 - prepare_colabfold_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
actions_schema_validation - actions_schema_validation
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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 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.mode= alphafold2
nextflow_config - Config default value correct: params.uniref30_prefix= UniRef30_2023_02
nextflow_config - Config default value correct: params.alphafold2_max_template_date= 2038-01-19
nextflow_config - Config default value correct: params.alphafold2_mode= split_msa_prediction
nextflow_config - Config default value correct: params.alphafold2_model_preset= monomer_ptm
nextflow_config - Config default value correct: params.alphafold2_params_prefix= alphafold_params_2022-12-06
nextflow_config - Config default value correct: params.colabfold_num_recycles= 3
nextflow_config - Config default value correct: params.colabfold_use_amber= true
nextflow_config - Config default value correct: params.colabfold_use_templates= false
nextflow_config - Config default value correct: params.colabfold_params_prefix= alphafold_params_2022-12-06
nextflow_config - Config default value correct: params.esmfold_num_recycles= 4
nextflow_config - Config default value correct: params.boltz_use_kernels= true
nextflow_config - Config default value correct: params.skip_foldseek= true
nextflow_config - Config default value correct: params.helixfold3_precision= bf16
nextflow_config - Config default value correct: params.helixfold3_infer_times= 4
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.alphafold2_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://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.fa.gz
nextflow_config - Config default value correct: params.alphafold2_pdb70_link= https://wwwuser.gwdguser.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_from_mmcif_220313.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.alphafold2_pdb_obsolete_link= https://files.wwpdb.org/pub/pdb/data/status/obsolete.dat
nextflow_config - Config default value correct: params.alphafold2_uniref30_link= https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.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.alphafold2_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.alphafold2_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.alphafold2_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.alphafold2_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.alphafold2_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.alphafold3_uniprot_link= https://storage.googleapis.com/alphafold-databases/v3.0/uniprot_all_2021_04.fa.zst
nextflow_config - Config default value correct: params.alphafold3_rnacentral_link= https://storage.googleapis.com/alphafold-databases/v3.0/rnacentral_active_seq_id_90_cov_80_linclust.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_nt_rna_link= https://storage.googleapis.com/alphafold-databases/v3.0/nt_rna_2023_02_23_clust_seq_id_90_cov_80_rep_seq.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_rfam_link= https://storage.googleapis.com/alphafold-databases/v3.0/rfam_14_9_clust_seq_id_90_cov_80_rep_seq.fasta.zst
nextflow_config - Config default value correct: params.alphafold3_small_bfd_path= null/small_bfd/*
nextflow_config - Config default value correct: params.alphafold3_mgnify_path= null/mgnify/*
nextflow_config - Config default value correct: params.alphafold3_pdb_mmcif_path= null/pdb_mmcif/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.alphafold3_rnacentral_path= null/rnacentral/*
nextflow_config - Config default value correct: params.alphafold3_nt_rna_path= null/nt_rna/*
nextflow_config - Config default value correct: params.alphafold3_rfam_path= null/rfam/*
nextflow_config - Config default value correct: params.colabfold_db_link= https://opendata.mmseqs.org/colabfold/colabfold_envdb_202108.db.tar.gz
nextflow_config - Config default value correct: params.colabfold_uniref30_link= https://opendata.mmseqs.org/colabfold/uniref30_2302.db.tar.gz
nextflow_config - Config default value correct: params.colabfold_alphafold2_params_link= https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar
nextflow_config - Config default value correct: params.colabfold_envdb_path= null/colabfold_envdb/*
nextflow_config - Config default value correct: params.colabfold_uniref30_path= null/colabfold_uniref30/*
nextflow_config - Config default value correct: params.colabfold_alphafold2_params_path= null/params/alphafold_params_2022-12-06
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.rosettafold2na_uniref30_link= http://wwwuser.gwdg.de/~compbiol/uniclust/2020_06/UniRef30_2020_06_hhsuite.tar.gz
nextflow_config - Config default value correct: params.rosettafold2na_bfd_link= https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
nextflow_config - Config default value correct: params.rosettafold2na_pdb100_link= https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
nextflow_config - Config default value correct: params.rosettafold2na_weights_link= https://files.ipd.uw.edu/dimaio/RF2NA_apr23.tgz
nextflow_config - Config default value correct: params.rfam_full_region_link= ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.full_region.gz
nextflow_config - Config default value correct: params.rfam_cm_link= ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz
nextflow_config - Config default value correct: params.rnacentral_rfam_annotations_link= ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/rfam/rfam_annotations.tsv.gz
nextflow_config - Config default value correct: params.rnacentral_id_mapping_link= ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/id_mapping/id_mapping.tsv.gz
nextflow_config - Config default value correct: params.rnacentral_sequences_link= ftp://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/sequences/rnacentral_species_specific_ids.fasta.gz
nextflow_config - Config default value correct: params.rosettafold2na_uniref30_path= null/UniRef30_2020_06/*
nextflow_config - Config default value correct: params.rosettafold2na_bfd_path= null/bfd/*
nextflow_config - Config default value correct: params.rosettafold2na_pdb100_path= null/pdb100/*
nextflow_config - Config default value correct: params.rosettafold2na_weights_path= null/params/network/weights/RF2NA_apr23.pt
nextflow_config - Config default value correct: params.rosettafold2na_rna_path= null/RNA/*
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.rosettafold_all_atom_uniref30_link= https://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_hhsuite.tar.gz
nextflow_config - Config default value correct: params.rosettafold_all_atom_bfd_link= https://bfd.mmseqs.com/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz
nextflow_config - Config default value correct: params.rosettafold_all_atom_pdb100_link= https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
nextflow_config - Config default value correct: params.rosettafold_all_atom_paper_weights_link= http://files.ipd.uw.edu/pub/RF-All-Atom/weights/RFAA_paper_weights.pt
nextflow_config - Config default value correct: params.rosettafold_all_atom_uniref30_path= null/uniref30/*
nextflow_config - Config default value correct: params.rosettafold_all_atom_bfd_path= null/bfd/*
nextflow_config - Config default value correct: params.rosettafold_all_atom_pdb100_path= null/pdb100/*
nextflow_config - Config default value correct: params.rosettafold_all_atom_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://wwwuser.gwdguser.de/~compbiol/uniclust/2023_02/UniRef30_2023_02_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://ftp.ebi.ac.uk/pub/databases/metagenomics/peptide_database/2024_04/mgy_clusters.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
nextflow_config - Config default value correct: params.helixfold3_maxit_src_link= https://proteinfold-dataset.s3.amazonaws.com/test-data/db/helixfold3/maxit-v11.200-prod-src.tar.gz
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/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/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/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_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/rosettafold_all_atom.nf.test' contains outdir parameter
nf_test_content - 'tests/rosettafold_all_atom.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rosettafold_all_atom.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/boltz.nf.test' contains outdir parameter
nf_test_content - 'tests/boltz.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/boltz.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/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/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/helixfold3.nf.test' contains outdir parameter
nf_test_content - 'tests/helixfold3.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/helixfold3.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rosettafold2na.nf.test' contains outdir parameter
nf_test_content - 'tests/rosettafold2na.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rosettafold2na.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: 25.10.2, Config: 25.10.2
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
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 - GENERATE_REPORT 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-03-19 00:32:36

sblaizerwize and others added 30 commits March 12, 2026 11:49

Included meta.yml file for the run_boltz module of the nf-core/protei…

12eee68

…nfold pipiline

Fix linting using pre-commit

e2f5849

Create meta.ym file for the local run_boltz module

2cc8389

Included meta.yml file for the run_boltz module of the nf-core/protei…

Started spinoff of extract_metrics as its own process

6e8bac0

Linted

0366ea3

Updated changelog

16e0970

Updated snapshots

4d6f92f

Removed vestigial container

804c81d

Included meta.yml file for run_alphafold2 module

d97f3b3

Fixed linting

70edcb9

Merge pull request #560 from sblaizerwize/my_contributions

a2cb936

Included meta.yml file for run_alphafold2 module

Merge branch 'dev' into hackathon_march_2026

14eb2ff

Merge branch 'hackathon_march_2026' into split-extract_metrics

4a632d8

Update CHANGELOG.md

7519e6d

Merge pull request #549 from nf-core/split-extract_metrics

3a1e3ff

Split extract_metrics for AlphaFold2

autodetect multimer in alphafold2 and esmfold

df74bd5

remove manual override of monomer and multimer presets

620f367

linting

bc003f8

update usage

5863ba6

fix colabfold auto detect multimer with existing dbs

14a2807

fix routing of colabfold params

8907737

fix fasta validation on split and cleanup

44ae392

update changelog

b3d5943

fix colabfold params download output config

2ca0ff4

harmonise colabfold params with alphafold2

9a32b76

fix linting

01975d7

fix merge conflicts

67a680d

fix hidden usage docs

18f120c

fix prepare colabfold dbs params

484b1b8

Split extract_metrics for HelixFold3

57b8e7a

Updated snapshots

5b747ef

jscgh self-assigned this Mar 18, 2026

jscgh added this to Hackathon March 2026 Mar 18, 2026

jscgh added enhancement Improvement for existing functionality Ready for review labels Mar 18, 2026

jscgh added 3 commits March 18, 2026 18:22

Changelog

8bb0662

Snapshots

7eeaba7

Snapshots

e1735c4

jscgh removed the Ready for review label Mar 19, 2026

jscgh force-pushed the hackathon_march_2026 branch from 484b1b8 to 2057b9d Compare April 16, 2026 06:08

jscgh added the WIP Work in progress label Apr 16, 2026

jscgh added this to the 3.0.0 milestone Apr 23, 2026

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Split extract metrics for HelixFold3#566

Split extract metrics for HelixFold3#566
jscgh wants to merge 34 commits intohackathon_march_2026from
split-extract_metrics-hf3

jscgh commented Mar 18, 2026 •

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❗ Test warnings:

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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jscgh commented Mar 18, 2026 •

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