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Add support for foldmason Guidetree and visualization #179

Merged
merged 61 commits into from
Dec 19, 2024
Merged

Add support for foldmason Guidetree and visualization #179

merged 61 commits into from
Dec 19, 2024

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luisas
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@luisas luisas commented Dec 9, 2024 •
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Here:

  • remove module mafft ( now it is mafft/align and mafft/guidetree, it should have been removed in a prev. PR)
  • add the visualization subworkflow (currently only supports foldmason visualization)
  • add the possibility to input guidetrees in foldmason. To do so, if PDBs only are provided, the fasta will be extracted from the pdbs.
  • Add a fasta validator for the input fasta
  • add a PDB preprocessing - this will homogenize the header (using a coffee module) so that is compatible with most downstream software (especially foldmason, will crush on PDBs from PDB if not preprocessed, works fine on all AF2 models)
  • move the merging in groovy: the final csv with the scientific accuracy metrics and the trace file are now merged on complete and directly fed to shiny.

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/multiplesequencealign 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).

@luisas luisas changed the base branch from master to dev December 9, 2024 10:07
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github-actions bot commented Dec 9, 2024 •
edited by nf-core-bot
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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: 3.0.2.
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.

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github-actions bot commented Dec 9, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5323ff5

+| ✅ 184 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-multiplesequencealign_logo_dark.png">\n <img alt="nf-core/multiplesequencealign" src="docs/images/nf-core-multiplesequencealign_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/multiplesequencealign 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 \n\n1. Read QC (FastQC)\n2. 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/multiplesequencealign \\\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/multiplesequencealign was originally written by Luisa Santus, Jose Espinosa Carrasco.\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 #multiplesequencealign 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/multiplesequencealign 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",
  • schema_params - Schema param genome not found from nextflow config
  • schema_params - Schema param fasta not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.0
  • Run at 2024-12-19 14:35:33

This was referenced Dec 9, 2024
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luisas and others added 25 commits December 19, 2024 15:04
@luisas @mirpedrol
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Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
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@luisas @JoseEspinosa
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Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
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luisas commented Dec 19, 2024

Also please update changelog!

Done :)

JoseEspinosa
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Awesome job thanks! 🚀

@luisas luisas merged commit 015b602 into nf-core:dev Dec 19, 2024
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@mirpedrol mirpedrol mirpedrol approved these changes

@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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