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Quantification#3

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leandrotiburske merged 6 commits intodevfrom
quantification
Jan 30, 2026
Merged

Quantification#3
leandrotiburske merged 6 commits intodevfrom
quantification

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@leandrotiburske
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@leandrotiburske leandrotiburske commented Jan 12, 2026

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 pipelines 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).

@leandrotiburske leandrotiburske changed the title Implement quantification with featureCounts Quantification Jan 12, 2026
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github-actions bot commented Jan 12, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0818ef8

+| ✅ 184 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗  26 tests had warnings |!
Details

❗ 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 nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • 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 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • 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
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  • 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 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 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 output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-nanotranseq_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nanotranseq_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-nanotranseq_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
  • 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: .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: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/nf-core-nanotranseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nanotranseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-nanotranseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/nanotranseq/nanotranseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-01-30 14:16:33

@leandrotiburske
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leandrotiburske commented Jan 13, 2026

Hi @matbonfanti and @karlaarz !

Here's an implementation of quantification!

Just a few points:

  1. As we discussed in the previous PR, I used params.quantification_tool directly instead of a channel due to differing validation times;

  2. For Salmon, I had to use reads as input instead of Minimap2's BAM files (alignment_mode=false), since those are not compatible with Salmon. Because of that, I decided to skip Minimap2 if Salmon is being used

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karlaarz commented Jan 13, 2026

Hi @leandrotiburske!

Seems pretty nice! A couple of things to highlight in these steps:

It might be worth it to add, after Salmon's quantification, the TXIMETA_TXIMPORT and CUSTOM_TX2GENE modules to get the count matrix from Salmon's output to be compatible with R.

Also, just an idea, but we can consider splitting the quantification into two. For instance, in the alignment subworkflow, we can add the quantification from subread as it uses minimap2 BAM files. Whereas for salmon quantification, we can name it as pseudo_alignment and pass only salmon quant and the tximport modules.

You can check the nf-core subworkflow QUANTIFY_PSEUDO_ALIGNMENT for a better insight.

We can also discuss this tomorrow :)

Base automatically changed from alignment to initial-modules January 14, 2026 13:28
Base automatically changed from initial-modules to dev January 14, 2026 13:30
@leandrotiburske
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leandrotiburske commented Jan 20, 2026

Hi @karlaarz !

I followed your suggestions, thank you for your input! I was having a lot of problems with TXIMPORT, but it somehow was fixed after I changed my Docker settings. It was probably something RAM-related 😅

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leandrotiburske commented Jan 30, 2026 •
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Hi @karlaarz !

I've replaced STRINGTIE_STRINGTIE by STRINGTIE2 from nanoseq as we discussed.

Also, I've changed the logic around pychopper! I know maybe I should've done it in a different PR, but since it's such a small change I did it here anyways :)
By default, direct_rna is set to true when testing, which ends up skipping the DIRECT_RNA subworkflow. Since it's pretty much the same asraw_read_qc, I think we can leave it like that for now (specially because FASTQC takes ages to run locally)

What do you think?

karlaarz
karlaarz reviewed Jan 30, 2026
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Hi @leandrotiburske ! looks better, we can merge it to the main branch. I will create a subworkflow for stringtie2 + gffcompare.

@leandrotiburske leandrotiburske merged commit 48c8132 into dev Jan 30, 2026
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