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Patch fastqscreen to handle multiple input FASTQ files #71

Merged
merged 9 commits into from
Dec 19, 2024
Merged

Patch fastqscreen to handle multiple input FASTQ files #71

merged 9 commits into from
Dec 19, 2024

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adamrtalbot
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@adamrtalbot adamrtalbot commented Dec 17, 2024 •
edited by kedhammar
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Fix for #70.

This will allow fastqscreen to handle any number of FASTQ files.

  • If there is 1 FASTQ file, the output will be called ${prefix}_screen.txt
  • If there is >1 FASTQ file, the output will be ${prefix}_${original file name}_screen.txt` to disambiguate it.

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).
    • One test for the AWS CI is failing, but probably out of scope for this PR.
  • 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).

@adamrtalbot adamrtalbot linked an issue Dec 17, 2024 that may be closed by this pull request
fastqscreen/fastqscreen can't handle >1 FASTQ file #70
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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 17, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e2d54ea

+| ✅ 172 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  22 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 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 \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/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 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 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!
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_unchanged - Required pipeline config not found - {'manifest.author'}

✅ Tests passed:

Run details

  • nf-core/tools version 3.1.0
  • Run at 2024-12-19 11:14:10

@kedhammar
Bugfix
126d1e3 
The file extensions were a bit wonky. Likely due to hasty copy-pasty :)
@kedhammar
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Thanks for this contribution!

I added a bugfix for the file extensions.

As for the naming of the output files when handling dual reads, I feel like it might be more readable to simply append _1 and _2 to the output filenames rather than appending the entire simpleName of the corresponding .fastq file?

What do you think?

@adamrtalbot
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Do you know how to do that?

@adamrtalbot
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Don't have time today to fix this, but yes adding an integer makes sense.

You might be able to use eachWithIndex instead of collect?

@kedhammar
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Do you know how to do that?

Not prior 😆

Don't have time today to fix this, but yes adding an integer makes sense.

You might be able to use eachWithIndex instead of collect?

I took a stab at it 🔪 bd8735e

adamrtalbot
adamrtalbot commented Dec 18, 2024
View reviewed changes
modules/nf-core/fastqscreen/fastqscreen/main.nf
def file_extensions = ['txt', 'html', 'png']
def mv_cmd = file_extensions.collect { ext ->
reads.withIndex().collect { read, i ->
"mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}"
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Nice!

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I'm happy with it if you are, you get to review your own code 😆

Or we get a third person to check it out.

adamrtalbot
adamrtalbot commented Dec 19, 2024
View reviewed changes
.github/workflows/branch.yml Outdated
Comment on lines 37 to 39
It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch.
The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
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Why not open a separate PR for all of this stuff?

@kedhammar
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Why not open a separate PR for all of this stuff?

I wanted to pass the linting prior to merging 😄 but now dev is updated and all tests are passing.

Feel free to merge at will if you are happy with it

@adamrtalbot adamrtalbot merged commit 1f7dc68 into nf-core:dev Dec 19, 2024
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@adamrtalbot adamrtalbot deleted the fastqscreen_handles_more_than_1_fastq_file branch December 19, 2024 11:20
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@kedhammar kedhammar kedhammar approved these changes

@MatthiasZepper MatthiasZepper Awaiting requested review from MatthiasZepper

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fastqscreen/fastqscreen can't handle >1 FASTQ file
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