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Add functionality to parse run dir metadata #106

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@kedhammar kedhammar commented Mar 25, 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/seqinspector branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • 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).

@kedhammar kedhammar added the enhancement New feature or request label Mar 25, 2025
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github-actions bot commented Mar 25, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fabdac5

+| ✅ 194 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  30 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in README.md: TODO nf-core:
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in ro-crate-metadata.json: "description": "

    \n \n <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-seqinspector_logo_dark.png">\n <img alt="nf-core/seqinspector" src="docs/images/nf-core-seqinspector_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/seqinspector 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/seqinspector \\\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/seqinspector was originally written by Adrien Coulier.\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 #seqinspector 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/seqinspector 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 test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • 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 meta.yml: #Add a description of the module and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a description and other details for the software below
  • pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
  • pipeline_todos - TODO string in meta.yml: #Delete / customise this example input
  • pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as output
  • pipeline_todos - TODO string in meta.yml: #Delete / customise this example output
  • pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
  • pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used
  • pipeline_todos - TODO string in main.nf.test: If you are created a test for a chained module
  • pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
  • pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
  • pipeline_todos - TODO string in main.nf.test: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
  • pipeline_todos - TODO string in main.nf.test: define inputs of the process here. Example:
  • pipeline_todos - TODO string in main.nf.test: //Add all required assertions to verify the test output.
  • 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.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-26 16:33:53

@kedhammar
give mqc outputs the same name so they will be merged automatically i…
70cacab 
…n the multiqc report generation, make function take output name as cmd parameter
@kedhammar
actually, let the script differentiate between seq platforms and name…
f0999e8 
… the outfile accordingly, for proper downstream grouping
@kedhammar
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kedhammar commented Mar 26, 2025

Ties into nf-core/test-datasets#1559

@matrulda matrulda mentioned this pull request Mar 26, 2025
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@maxulysse maxulysse added this to the 1.0.0 milestone Nov 6, 2025
@FranBonath FranBonath mentioned this pull request Nov 7, 2025
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@matrulda
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matrulda commented Nov 25, 2025

Current status: The module is working - currently only supporting Illumina runfolders, I think that is an OK scope for v1.
I've updated pipeline tests and they run ok, but still have issues with the module test. I've added my current progress with them as a "WIP" commit.

@maxulysse If you have time later this week, would you mind having a look at modules/local/rundirparser/tests/main.nf.test and give some advice?

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maxulysse commented Nov 25, 2025

Current status: The module is working - currently only supporting Illumina runfolders, I think that is an OK scope for v1. I've updated pipeline tests and they run ok, but still have issues with the module test. I've added my current progress with them as a "WIP" commit.

@maxulysse If you have time later this week, would you mind having a look at modules/local/rundirparser/tests/main.nf.test and give some advice?

I can see that the pipeline tests are failing with:

mkdir: cannot create directory ‘test_rundir’: File exists

I would investigate the logic in the module script

    if [ ! -d test_rundir ]; then
        mkdir -p test_rundir
    fi

Have you managed to run the module or the test locally?

Could you investigate the workdir for the task, and see what happens with this test_rundir folder

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