Add RFAA and HF3 modules #26

jscgh · 2024-12-02T05:59:16Z

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).

Visualisation

comparison report

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update comparison report

Visualisation

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github-actions · 2024-12-02T06:02:11Z

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

Posted for pipeline commit 2ff94c3

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

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
pipeline_todos - TODO string in 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 · 2024-12-05T00:11:27Z

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

nbtm-sh · 2024-12-05T04:07:27Z

Running HF3 I get this output:
output.log

jscgh · 2024-12-05T04:29:55Z

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 · 2024-12-06T03:55:44Z

Tests completed fine. Looks good to me

minh-biocommons and others added 30 commits October 11, 2024 12:04

UI changes

e198f91

UI changes

327db82

button spacing

17b65b1

buttons

2548f9a

Draft new file: run_helixfold3.nf

f8b8f4e

Cleaned up folders

4b3bd9e

Merge pull request #4 from minh-biocommons/visualisation

c065073

Visualisation

comparison report

623ba89

tweak

6c584ce

Merge pull request #5 from minh-biocommons/visualisation

11befcb

comparison report

Merge pull request #6 from ziadbkh/visualisation

df3595a

add comparision report

update comparison report

448a1db

Merge pull request #7 from minh-biocommons/visualisation

f3e7420

update comparison report

Merge pull request #8 from ziadbkh/visualisation

e5e7a8a

Visualisation

compdaare structures

c0315f7

Merge branch 'dev' of https://github.com/ziadbkh/proteinfold into vis…

96c8d40

…ualisation2

adding the comparision to the main workflow

64a273a

fix structure alignment

1928cc9

minor fixes

8b1038e

view channels

2a10d57

fix channel names

bee5176

update report

bb7b6a4

update button

08cbbf9

Merge pull request #9 from minh-biocommons/visualisation2

0aff7aa

update report

update reports

39ba331

change output names

12ff501

Merge branch 'nf-core:dev' into dev

118b531

merging dev

e39c585

fix output names

12ea327

fix output names

8db00cb

jscgh added 10 commits November 29, 2024 15:58

Aligned with nf-core dev

d64b9f1

Merge remote-tracking branch 'upstream/dev' into add-helixfold3

17e40bf

Merge remote-tracking branch 'upstream/dev' into add-rosettafold-all-…

3dc1448

…atom

Merge branch 'add-helixfold3' into nfcore-dev

5da1437

Merge remote-tracking branch 'origin/add-rosettafold-all-atom' into n…

d86c5c2

…fcore-dev

Merged add-rosettafold-all-atom and add-helixfold3

7bb1ff4

Fixed typo

5834677

Linted

c257cd6

Fixed post_processing channels

d7d25f9

Adding HF3 to generate_report.py

d5f59c4

jscgh added the enhancement New feature or request label Dec 2, 2024

jscgh requested review from keiran-rowell-unsw and nbtm-sh December 2, 2024 05:59

jscgh added 7 commits December 3, 2024 11:31

Prettier

b9229d3

RFAA Dockerfile added

5ac95e4

RFAA Dockerfile added

0d36668

Updated RFAA Dockerfile path

085175b

modified: dockerfiles/Dockerfile_nfcore-proteinfold_rosettafold_all_atom

5b602a3

RFAA Dockerfile builds

b647bc1

RFAA Dockerfile working successfully

2ff94c3

Added HF3 dockerfile

8947eb4

jscgh added 2 commits December 5, 2024 16:15

Fixed HF3 dockerfile

9b11a62

Updated rfaa def file from branch

8b202b9

nbtm-sh approved these changes Dec 6, 2024

View reviewed changes

jscgh merged commit 3bba62b into unsw-dev Dec 6, 2024
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Add RFAA and HF3 modules #26

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jscgh commented Dec 2, 2024

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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