Updated images for splitting ColabFold

Open jscgh opened this issue 3 months ago • 2 comments

mmseqs_colabfoldsearch and colabfold_batch now have separate Dockerfiles
The mmseqs_colabfoldsearch image is now much slimmer, useful when pulling for non colabfold_batch modes e.g. Boltz
The colabfold_batch image size has also been significantly reduced
ColabFold pinned to commit e8ebd9a for reproducibility
CUDA upgraded to 12.9.1 with JAX 0.5.3 GPU support

ColabFold mini databases for testing are available here. Prebuilt images are available at ghcr.io/jscgh/proteinfold_colabfold:dev and ghcr.io/jscgh/proteinfold_mmseqs_colabfoldsearch:dev

PR checklist

[x] This comment contains a description of changes (with reason).
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[x] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[x] CHANGELOG.md is updated.

Oct 02 '25 06:10 jscgh

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit cbcb9ab

+| ✅ 324 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  19 tests had warnings |!

:heavy_exclamation_mark: 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 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 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 nextflow.config: Specify any additional parameters here
local_component_structure - post_processing.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_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 - aria2_uncompress.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_helixfold3_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_alphafold2_dbs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

:grey_question: 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

:white_check_mark: 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 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.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_model_preset= alphafold2_ptm
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= true
nextflow_config - Config default value correct: params.esmfold_num_recycles= 4
nextflow_config - Config default value correct: params.esmfold_model_preset= monomer
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_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/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_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.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.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/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/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/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/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/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/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/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/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: 25.04.0, Config: 25.04.0
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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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: 3.4.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.4.1
Run at 2025-11-17 23:17:58

Oct 02 '25 06:10 github-actions[bot]

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2. 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.

Oct 17 '25 06:10 nf-core-bot

Updated images for splitting ColabFold

PR checklist

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

:heavy_exclamation_mark: Test warnings:

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning: