Add RFAA and HF3 modules

[jscgh]

• Combines the add-rosettafold-all-atom and add-helixfold3 branches
• Merged with nf-core/dev

PR checklist

• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,**singularity** --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,**singularity** --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 2ff94c3

+| ✅ 251 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  44 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes.config
• files_exist - File not found: conf/igenomes_ignored.config
• 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 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
• schema_description - Ungrouped param in schema: helixfold3_init_models_link
• schema_description - Ungrouped param in schema: helixfold3_init_models_path
• schema_description - Ungrouped param in schema: helixfold3_db
• schema_description - Ungrouped param in schema: helixfold3_uniclust30_link
• schema_description - Ungrouped param in schema: helixfold3_ccd_preprocessed_link
• schema_description - Ungrouped param in schema: helixfold3_rfam_link
• schema_description - Ungrouped param in schema: helixfold3_bfd_link
• schema_description - Ungrouped param in schema: helixfold3_small_bfd_link
• schema_description - Ungrouped param in schema: helixfold3_pdb_seqres_link
• schema_description - Ungrouped param in schema: helixfold3_uniref90_link
• schema_description - Ungrouped param in schema: helixfold3_mgnify_link
• schema_description - Ungrouped param in schema: helixfold3_pdb_mmcif_link
• schema_description - Ungrouped param in schema: helixfold3_uniclust30_path
• schema_description - Ungrouped param in schema: helixfold3_ccd_preprocessed_path
• schema_description - Ungrouped param in schema: helixfold3_rfam_path
• schema_description - Ungrouped param in schema: helixfold3_bfd_path
• schema_description - Ungrouped param in schema: helixfold3_small_bfd_path
• schema_description - Ungrouped param in schema: helixfold3_uniprot_path
• schema_description - Ungrouped param in schema: helixfold3_pdb_seqres_path
• schema_description - Ungrouped param in schema: helixfold3_uniref90_path
• schema_description - Ungrouped param in schema: helixfold3_mgnify_path
• schema_description - Ungrouped param in schema: helixfold3_pdb_mmcif_path
• schema_description - Ungrouped param in schema: helixfold3_uniprot_sprot_link
• schema_description - Ungrouped param in schema: helixfold3_uniprot_trembl_link
• schema_description - Ungrouped param in schema: helixfold3_pdb_obsolete_link
• schema_description - Ungrouped param in schema: helixfold3_maxit_src_path
• schema_description - Ungrouped param in schema: rosettafold_all_atom_db
• schema_description - Ungrouped param in schema: uniref30_rosettafold_all_atom_link
• schema_description - Ungrouped param in schema: pdb100_rosettafold_all_atom_link
• schema_description - Ungrouped param in schema: bfd_rosettafold_all_atom_path
• schema_description - Ungrouped param in schema: rfaa_paper_weights_link
• schema_description - Ungrouped param in schema: uniref30_rosettafold_all_atom_path
• schema_description - Ungrouped param in schema: pdb100_rosettafold_all_atom_path
• schema_description - Ungrouped param in schema: rfaa_paper_weights_path
• schema_description - Ungrouped param in schema: bfd_rosettafold_all_atom_link

❔ 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_ci - actions_ci
• 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: .editorconfig
• 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/ci.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: 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 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.helixfold3_init_models_link= https://paddlehelix.bd.bcebos.com/HelixFold3/params/HelixFold3-params-240814.zip
• nextflow_config - Config default value correct: params.helixfold3_init_models_path= null/HelixFold3-240814.pdparams
• 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_uniclust30_path= null/uniclust30/*
• nextflow_config - Config default value correct: params.helixfold3_ccd_preprocessed_path= null/ccd_preprocessed_etkdg.pkl.gz
• nextflow_config - Config default value correct: params.helixfold3_rfam_path= null/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/*
• 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_pdb_obsolete_link= ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat
• nextflow_config - Config default value correct: params.helixfold3_maxit_src_path= null/maxit-v11.200-prod-src
• 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.pdb100_rosettafold_all_atom_link= https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
• nextflow_config - Config default value correct: params.bfd_rosettafold_all_atom_path= null/bfd/*
• 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/UniRef30_2020_06/*
• nextflow_config - Config default value correct: params.pdb100_rosettafold_all_atom_path= null/pdb100_2021Mar03/*
• nextflow_config - Config default value correct: params.rfaa_paper_weights_path= null/RFAA_paper_weights.pt
• 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.mode= alphafold2
• nextflow_config - Config default value correct: params.max_template_date= 2020-05-14
• 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.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.db_load_mode= 0
• 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.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.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.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.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.uniref30_alphafold2_link= https://storage.googleapis.com/alphafold-databases/v2.3/UniRef30_2021_03.tar.gz
• nextflow_config - Config default value correct: params.uniref90_link= https://ftp.ebi.ac.uk/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz
• nextflow_config - Config default value correct: params.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.small_bfd_path= null/small_bfd/*
• nextflow_config - Config default value correct: params.alphafold2_params_path= null/alphafold_params_/
• nextflow_config - Config default value correct: params.mgnify_path= null/mgnify/*
• nextflow_config - Config default value correct: params.pdb70_path= null/pdb70/**
• nextflow_config - Config default value correct: params.pdb_mmcif_path= null/pdb_mmcif/*
• nextflow_config - Config default value correct: params.uniref30_alphafold2_path= null/uniref30/*
• nextflow_config - Config default value correct: params.uniref90_path= null/uniref90/*
• nextflow_config - Config default value correct: params.pdb_seqres_path= null/pdb_seqres/*
• nextflow_config - Config default value correct: params.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.uniref30_colabfold_link= https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gz
• nextflow_config - Config default value correct: params.colabfold_db_path= null/colabfold_envdb_202108
• nextflow_config - Config default value correct: params.uniref30_colabfold_path= null/uniref30_2302
• 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/*
• 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/
• 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_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 Zenodo placeholder was replaced with DOI.
• 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: branch.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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'
• 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: 3.0.2

Run details

• nf-core/tools version 3.0.2
• Run at 2024-12-04 23:25:51

[nbtm-sh]

Will run tests through OnDemand later today. Keep you posted!

[nbtm-sh]

Running HF3 I get this output:
output.log

[jscgh]

Seems to be from Message: "Could not open file: ./maxit_src/data/binary/variant.odb" generated at: BlockIO::OpenFile

Permissions error on the DBs.
-rw-------. 1 z5378336 sbf 1.9M Sep 10 16:18 variant.odb
Should be fixed now.

[nbtm-sh]

Tests completed fine. Looks good to me