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@ziadbkh ziadbkh commented Dec 4, 2024 •
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Adding a docker file to run boltz with ProteinFOld

PR checklist

  • 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).

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github-actions bot commented Dec 4, 2024 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 9cd6b2d

+| ✅ 249 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  62 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - assets/nf-core-proteinfold_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-proteinfold_logo_light.png does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • files_unchanged - LICENSE does not match the template
  • 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\nGitHub Actions CI Status\nGitHub Actions Linting StatusAWS CICite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\nGet help on SlackFollow on TwitterFollow on MastodonWatch on YouTube\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 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.
  • 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!
  • 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: 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_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_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: 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
  • local_component_structure - post_processing.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_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_alphafold2_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 - prepare_rosettafold_all_atom_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

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.1
  • Run at 2025-05-01 07:39:24

nbtm-sh and others added 2 commits February 6, 2025 10:02
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nf-core-bot commented Feb 5, 2025 •
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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.

JoseEspinosa
JoseEspinosa reviewed Feb 18, 2025
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Just wanted to confirm that it is enough to install boltz from pip to create a working image with @nbtm-sh, before approving this PR, thanks!

@ziadbkh
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ziadbkh commented Feb 27, 2025

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

@nbtm-sh
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nbtm-sh commented Mar 7, 2025

@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.

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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.

@JoseEspinosa JoseEspinosa added this to the 1.3.0 milestone Mar 25, 2025
@ziadbkh ziadbkh changed the title docker file for boltz Adding boltz model Apr 29, 2025
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