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Update arriba#693

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rannick merged 25 commits intodevfrom
update_arriba
Jul 15, 2025
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Update arriba#693
rannick merged 25 commits intodevfrom
update_arriba

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@rannick rannick commented Jul 4, 2025

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/rnafusion branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • 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).

@rannick rannick changed the base branch from master to dev July 4, 2025 11:41
@nf-core nf-core deleted a comment from github-actions bot Jul 4, 2025
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github-actions bot commented Jul 4, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ba3c86

+| ✅ 222 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ 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-rnafusion_logo_dark.png">\n <img alt="nf-core/rnafusion" src="docs/images/nf-core-rnafusion_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/rnafusion 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 nf-core/rnafusion \\\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/rnafusion was originally written by Martin Proks, Annick Renevey.\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 #rnafusion 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/rnafusion 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • schema_lint - Input mimetype is missing or empty
  • local_component_structure - fusioninspector_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.1
  • Run at 2025-07-15 07:12:31

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nf-core-bot commented Jul 4, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
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.

rannick and others added 22 commits July 8, 2025 10:23
@rannick rannick marked this pull request as ready for review July 15, 2025 07:08
nvnieuwk
nvnieuwk approved these changes Jul 15, 2025
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Good job!

@rannick rannick merged commit d0cef33 into dev Jul 15, 2025
10 checks passed
@rannick rannick deleted the update_arriba branch July 15, 2025 09:37
atrigila
atrigila reviewed Jul 17, 2025
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tests/test_build.nf.test
name "Test pipeline"
script "../main.nf"
profile "test_build"
options "-stub"
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@atrigila atrigila Jul 17, 2025

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I am sorry, but I do not understand why you added -stub here. I do not know if it was a temporal test or you forgot to remove that, but It is against the purpose of having a CI test that actually uses small input files and tests a bit of the first part of the pipeline without it being a stub.

tests/test_build.nf.test
Comment on lines +15 to +28
config_profile_name = 'Test build references profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

// Input data
references_only = true
input = "${projectDir}/tests/csv/fastq.csv"
no_cosmic = true
tools = "arriba,starfusion,fusionreport,salmon,fusioninspector"
fasta = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.fa'
gtf = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/minigenome.gtf'
fusion_annot_lib = 'https://github.com/STAR-Fusion/STAR-Fusion-Tutorial/raw/master/CTAT_HumanFusionLib.mini.dat.gz'
species = 'homo_sapiens'
dfam_version = '3.4'
outdir = "$outputDir"
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@atrigila atrigila Jul 17, 2025

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If you add params here, you override the params in profile "test_build".

tests/test_build.nf.test
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I think this test case should not be modified. If you would like a to add a stub test case for the test_build you can copy this one and add it as an additional one, but I think that having a working CI test with files is necessary for the pipeline. Issues are much more difficult to detect with only stub tests.

@atrigila atrigila mentioned this pull request Sep 16, 2025
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