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Update documentation

Open tlitfin-unsw opened this issue 5 months ago • 1 comments

  • Added mode-specific usage documentation.
  • Added table to README to demonstrate mode capabilities.

TODO:

  • [ ] Add new metro-map
  • [ ] Complete RF2NA docs when mode is merged
  • [ ] Update outputs documentation

PR checklist

  • [x] 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>).
  • [x] Usage Documentation in docs/usage.md is updated.
  • [x] Output Documentation in docs/output.md is updated.
  • [x] CHANGELOG.md is updated.
  • [x] README.md is updated (including new tool citations and authors/contributors).

tlitfin-unsw avatar Aug 03 '25 12:08 tlitfin-unsw

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

Posted for pipeline commit d400f10

+| ✅ 328 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:

: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: 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.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= http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.tar.gz
  • nextflow_config - Config default value correct: params.colabfold_uniref30_link= https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2302.tar.gz
  • nextflow_config - Config default value correct: params.colabfold_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: 24.10.5, Config: 24.10.5
  • 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: 3.3.2
  • rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-10-14 06:20:47

github-actions[bot] avatar Aug 03 '25 12:08 github-actions[bot]