docker file for boltz

Open ziadbkh opened this issue 1 year ago • 5 comments

Adding a docker file to run boltz with ProteinFOld

PR checklist

[x] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] If necessary, also make a PR on the nf-core/proteinfold branch on the nf-core/test-datasets repository.
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --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).

Dec 04 '24 03:12 ziadbkh

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

Posted for pipeline commit f766d6c

+| ✅ 256 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  63 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 ro-crate-metadata.json: "description": "
\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-proteinfold_logo_dark.png">\n <img alt="nf-core/proteinfold" src="docs/images/nf-core-proteinfold_logo_light.png">\n \n
\n\n\n \n\n\n\n\n\n\n\n\n \n\n## Introduction\n\nnf-core/proteinfold is a bioinformatics pipeline that ...\n\n TODO nf-core:\n Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the\n major pipeline sections and the types of output it produces. You're giving an overview to someone new\n to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction\n\n\n Include a figure that guides the user through the major workflow steps. Many nf-core\n workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. \n Fill in short bullet-pointed list of the default steps in the pipeline 2. Present QC for raw reads (MultiQC)\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.\n\n Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.\n Explain what rows and columns represent. For instance (please edit as appropriate):\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\nsamplesheet.csv:\n\ncsv\nsample,fastq_1,fastq_2\nCONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz\n\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\n\n\nNow, you can run the pipeline using:\n\n update the following command to include all required parameters for a minimal example \n\nbash\nnextflow run nf-core/proteinfold \\\n -profile <docker/singularity/.../institute> \\\n --input samplesheet.csv \\\n --outdir <OUTDIR>\n\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.\n\nFor more details and further functionality, please refer to the usage documentation and the parameter documentation.\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\noutput documentation.\n\n## Credits\n\nnf-core/proteinfold was originally written by Athanasios Baltzis, Jose Espinosa-Carrasco, Harshil Patel.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n If applicable, make list of people who have also contributed \n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the contributing guidelines.\n\nFor further information or help, don't hesitate to get in touch on the Slack #proteinfold channel (you can join with this invite).\n\n## Citations\n\n Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. \n If you use nf-core/proteinfold for your analysis, please cite it using the following doi: 10.5281/zenodo.XXXXXX \n\n Add bibliography of tools and data used in your pipeline \n\nAn extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.\n\nYou can cite the nf-core publication as follows:\n\n> The nf-core framework for community-curated bioinformatics pipelines.\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.\n",
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 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 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 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.
schema_description - No description provided in schema for parameter: random_seed
schema_description - No description provided in schema for parameter: rosettafold_all_atom_db
schema_description - No description provided in schema for parameter: helixfold3_db
schema_description - No description provided in schema for parameter: model_name
schema_description - No description provided in schema for parameter: preset
schema_description - No description provided in schema for parameter: init_model
schema_description - No description provided in schema for parameter: logging_level
schema_description - No description provided in schema for parameter: precision
schema_description - No description provided in schema for parameter: infer_times
schema_description - No description provided in schema for parameter: helixfold3_max_template_date
schema_description - No description provided in schema for parameter: uniref30_rosettafold_all_atom_link
schema_description - No description provided in schema for parameter: bfd_rosettafold_all_atom_link
schema_description - No description provided in schema for parameter: pdb100_rosettafold_all_atom_link
schema_description - No description provided in schema for parameter: rfaa_paper_weights_link
schema_description - No description provided in schema for parameter: uniref30_rosettafold_all_atom_path
schema_description - No description provided in schema for parameter: bfd_rosettafold_all_atom_path
schema_description - No description provided in schema for parameter: pdb100_rosettafold_all_atom_path
schema_description - No description provided in schema for parameter: rfaa_paper_weights_path
schema_description - No description provided in schema for parameter: helixfold3_init_models_path
schema_description - No description provided in schema for parameter: helixfold3_uniclust30_path
schema_description - No description provided in schema for parameter: helixfold3_ccd_preprocessed_path
schema_description - No description provided in schema for parameter: helixfold3_rfam_path
schema_description - No description provided in schema for parameter: helixfold3_bfd_path
schema_description - No description provided in schema for parameter: helixfold3_small_bfd_path
schema_description - No description provided in schema for parameter: helixfold3_uniprot_path
schema_description - No description provided in schema for parameter: helixfold3_pdb_seqres_path
schema_description - No description provided in schema for parameter: helixfold3_uniref90_path
schema_description - No description provided in schema for parameter: helixfold3_mgnify_path
schema_description - No description provided in schema for parameter: helixfold3_pdb_mmcif_path
schema_description - No description provided in schema for parameter: helixfold3_maxit_src_path
schema_description - No description provided in schema for parameter: helixfold3_obsolete_path
schema_description - No description provided in schema for parameter: helixfold3_init_models_link
schema_description - No description provided in schema for parameter: helixfold3_uniclust30_link
schema_description - No description provided in schema for parameter: helixfold3_ccd_preprocessed_link
schema_description - No description provided in schema for parameter: helixfold3_rfam_link
schema_description - No description provided in schema for parameter: helixfold3_bfd_link
schema_description - No description provided in schema for parameter: helixfold3_small_bfd_link
schema_description - No description provided in schema for parameter: helixfold3_pdb_seqres_link
schema_description - No description provided in schema for parameter: helixfold3_uniref90_link
schema_description - No description provided in schema for parameter: helixfold3_mgnify_link
schema_description - No description provided in schema for parameter: helixfold3_pdb_mmcif_link
schema_description - No description provided in schema for parameter: helixfold3_uniprot_sprot_link
schema_description - No description provided in schema for parameter: helixfold3_uniprot_trembl_link
schema_description - No description provided in schema for parameter: helixfold3_pdb_obsolete_link
schema_description - No description provided in schema for parameter: helixfold3_obsolete_link
local_component_structure - prepare_alphafold2_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 - 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_colabfold_dbs.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 - aria2_uncompress.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
actions_ci - actions_ci
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: .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 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.max_template_date= 2038-01-19
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.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.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/mmcif_files
nextflow_config - Config default value correct: params.pdb_obsolete_path= null/pdb_mmcif/obsolete.dat
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/
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.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.pdb100_rosettafold_all_atom_link= https://files.ipd.uw.edu/pub/RoseTTAFold/pdb100_2021Mar03.tar.gz
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.bfd_rosettafold_all_atom_path= null/bfd/*
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.helixfold3_init_models_path= null/HelixFold3-240814.pdparams
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/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://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_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
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
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files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
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files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - assets/email_template.html matches the template
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files_unchanged - assets/nf-core-proteinfold_logo_light.png matches the template
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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: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.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: template_version_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'
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: 3.2.1

Run details

nf-core/tools version 3.2.1
Run at 2025-05-15 09:33:21

Dec 04 '24 03:12 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: 3.2.0. 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.

Feb 05 '25 23:02 nf-core-bot

It seems it is. It works on our internal HPC and used the GPU

Feb 27 '25 02:02 ziadbkh

@JoseEspinosa sorry for the long delay in reply, been super bogged down. the cuda libraries are listed as dependencies for boltz, so installing it with pip will be enough for it to play nice with 99% of HPC stuff.

Mar 07 '25 02:03 nbtm-sh

No worries! Nice, anyway we won't merge this PR until the next release.

@JoseEspinosa sorry for the long delay in reply, been super bogged down. the cuda libraries are listed as dependencies for boltz, so installing it with pip will be enough for it to play nice with 99% of HPC stuff.

Mar 07 '25 08:03 JoseEspinosa

docker file for boltz

PR checklist

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

:heavy_exclamation_mark: Test warnings:

\n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-proteinfold_logo_dark.png">\n <img alt="nf-core/proteinfold" src="docs/images/nf-core-proteinfold_logo_light.png">\n \n

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

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