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Fixed the handling of the taxdump#146

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tkchafin merged 3 commits intodevfrom
taxdump
Mar 17, 2025
Merged

Fixed the handling of the taxdump#146
tkchafin merged 3 commits intodevfrom
taxdump

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@muffato muffato commented Mar 10, 2025 •
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Closes #134

JSON files are not generated in the input directory any more. They're generated in a separate location that is then passed to the downstream tools.
To make this more efficient, the pipeline can accept taking a JSON directly, or a taxdump directory that contains the JSON. I'll need to update the taxonomy download script on the farm.

Note: blobtoolkit requires the file to be named taxdump.json. I enforce that with the stageAs directive rather than when generating the file.

I also still want to:

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
  • 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).

@muffato
Fixed the handling of the taxdump
d005311 
JSON files are not generated in the input directory any more.
Importantly, the pipeline accepts taking a JSON in too.
@muffato muffato requested a review from DLBPointon March 10, 2025 09:44
@muffato muffato self-assigned this Mar 10, 2025
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github-actions Bot commented Mar 10, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8a53451

+| ✅ 180 tests passed       |+
#| ❔  28 tests were ignored |#
!| ❗  25 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config variable not found: validation.help.beforeText
  • nextflow_config - Config variable not found: validation.help.afterText
  • nextflow_config - Config variable not found: validation.summary.beforeText
  • nextflow_config - Config variable not found: validation.summary.afterText
  • nextflow_config - Config manifest.version should end in dev: 0.7.0
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "# sanger-tol/blobtoolkit\n\nGitHub Actions CI Status\nGitHub Actions Linting StatusCite with Zenodo\nnf-test\n\nNextflow\nrun with conda\nrun with docker\nrun with singularity\nLaunch on Seqera Platform\n\n## Introduction\n\nsanger-tol/blobtoolkit 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 1. Read QC (FastQC)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 sanger-tol/blobtoolkit \\\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\n## Credits\n\nsanger-tol/blobtoolkit was originally written by priyanka-surana.\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\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 sanger-tol/blobtoolkit 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\nThis pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.\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",
  • local_component_structure - jsonify_taxdump.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - create_bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - nohit_list.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - restructurebuscodir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - generate_config.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - compressblobdir.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - windowstats_input.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - run_blastx.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - view.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - collate_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - run_blastn.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - minimap_alignment.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - coverage_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - finalise_blobdir.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - blobtools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - busco_diamond_blastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-blobtoolkit_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-blobtoolkit_logo_dark.png
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/blobtoolkit/blobtoolkit/.github/workflows/awstest.yml
  • template_strings - template_strings
  • merge_markers - merge_markers

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-15 00:37:48

DLBPointon
DLBPointon approved these changes Mar 11, 2025
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Looks good to me, covers all the cases I can imagine happening.
Initial generation is something we could add to that setup pipeline if it goes ahead.

Base automatically changed from template_upgrade to first_precomp_busco March 14, 2025 11:05
@muffato muffato deleted the branch dev March 14, 2025 11:06
@muffato muffato closed this Mar 14, 2025
@muffato muffato reopened this Mar 14, 2025
@muffato muffato changed the base branch from first_precomp_busco to dev March 14, 2025 11:08
@muffato muffato changed the base branch from dev to first_template_upgrade March 14, 2025 11:34
@muffato muffato deleted the branch dev March 14, 2025 16:25
@muffato muffato closed this Mar 14, 2025
@muffato muffato reopened this Mar 14, 2025
@muffato muffato changed the base branch from first_template_upgrade to dev March 14, 2025 16:29
@muffato muffato force-pushed the taxdump branch 2 times, most recently from 6ecfdfe to 8a53451 Compare March 15, 2025 00:36
@muffato muffato marked this pull request as ready for review March 15, 2025 10:44
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muffato commented Mar 15, 2025

Ready for merging ! Latest changes:

  • JSON is now published, so that it can be reused
  • test the JSON on CI
  • I've updated our internal taxonomy download procedure to generate the JSON file
  • documentation updated

@muffato muffato mentioned this pull request Mar 15, 2025
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@tkchafin tkchafin merged commit 2500f11 into dev Mar 17, 2025
@tkchafin tkchafin deleted the taxdump branch March 17, 2025 10:30
@muffato muffato added this to the v0.7.0 milestone Feb 20, 2026
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