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New Feature - Flexible analysis start#55

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sguizard wants to merge 34 commits intodevfrom
feature-flexible_start
Open

New Feature - Flexible analysis start#55
sguizard wants to merge 34 commits intodevfrom
feature-flexible_start

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@sguizard sguizard commented Nov 1, 2025 •
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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/isoseq branch on the nf-core/test-datasets repository.
  • 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).

Isoseq providers deliver sequences in many different format depending of the pre-processing they apply (Subreqds, CCS, Full Length isoseq). This even more true with the new MAS-seq.
I had implemented the possibility to deals with these format through options. However, their usage along with the possibility to skip ISOseq processing and align made the samplesheet and the usage of the pipeline complex.

In this PR, I changed the way to inject input sequences into the pipeline. Now, it's possible start analysis from ccs, lima, isoseq refine or at the mapping step. The different types of inputs can be even mixed in the samplesheet.
This modification simplify the usage but also the code.

It not necessary to deals with the different entrypoints any more. The inputs files are injected at the right moment in the main channel paths.

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github-actions bot commented Nov 1, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 370ffb4

+| ✅ 256 tests passed       |+
!| ❗   5 tests had warnings |!
Details

❗ Test warnings:

  • 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 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 nextflow.config: Specify any additional parameters here

✅ Tests passed:

Run details

  • nf-core/tools version 3.4.1
  • Run at 2026-04-06 09:42:17

maxulysse
maxulysse reviewed Nov 3, 2025
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assets/schema_input.json
"errorMessage": "PacBio Index file for BAM subreads cannot contain spaces and must have extension '.bam.pbi' or being empty"
},
"reads": {
"start_from": {
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I think we can find a better name for this field

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@sguizard sguizard Nov 3, 2025 •
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I have been scratching my head for naming this.
I used entrypoint, but I didn't felt it was very clear for users.
'start_from' is might not be the best, at least, it's very clear on it's signification.

Do you have propositions?

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I use step in sarek, but it's a param, not in the samplesheet

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sguizard commented Nov 3, 2025

I added a subworflow to chunk the fasta files (from lima, isoseq refine and mapping start) before the mapping steps.
As those inputs files are devided into chunks with CCS, the fasta produced is massive and contains all sequences. To mitigate this problem, the CHUNKER subworkflow will split those into small chunks.

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sguizard commented Nov 10, 2025

A new update of the CHUNKER to apply it twice in the pipeline.

@sguizard sguizard added the WIP Work in progress label Nov 11, 2025
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sguizard commented Apr 6, 2026

Hi @maxulysse, I'm returning on isoseq analysis and I would like to merge this pull request before applying the last templates updates.
Can you have a look and indicates if the code need some corrections?

@sguizard sguizard removed the WIP Work in progress label Apr 6, 2026
maxulysse
maxulysse reviewed Apr 7, 2026
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nextflow.config
Comment on lines +192 to +204
test { includeConfig 'conf/test.config' }
test_minimap2 { includeConfig 'conf/test_minimap2.config' }
test_full { includeConfig 'conf/test_full.config' }
test_inputs_map { includeConfig 'conf/test_samplesheet_v2_map.config' }
test_inputs_lima { includeConfig 'conf/test_samplesheet_v2_lima.config' }
test_inputs_refine { includeConfig 'conf/test_samplesheet_v2_refine.config' }
test_inputs_ccs { includeConfig 'conf/test_samplesheet_v2_ccs.config' }
test_inputs_ccs_lima_refine_map_mergeAll { includeConfig 'conf/test_samplesheet_v2_ccs_lima_refine_map_mergeAll.config' }
test_inputs_ccs_lima_refine_map { includeConfig 'conf/test_samplesheet_v2_ccs_lima_refine_map.config' }
test_inputs_ccs_map { includeConfig 'conf/test_samplesheet_v2_ccs_map.config' }
test_inputs_lima_refine_map { includeConfig 'conf/test_samplesheet_v2_lima_refine_map.config' }
test_inputs_refine_map { includeConfig 'conf/test_samplesheet_v2_refine_map.config' }
test_inputs_multi_lib { includeConfig 'conf/test_samplesheet_v2_multi_lib.config' }
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I do tend to recommend less config files dedicated to test, and putting more or the logic in nf-test, but fine with me for now

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maxulysse commented Apr 7, 2026

Hi @maxulysse, I'm returning on isoseq analysis and I would like to merge this pull request before applying the last templates updates. Can you have a look and indicates if the code need some corrections?

I don't see anything weird, so fine by me

maxulysse
maxulysse approved these changes Apr 7, 2026
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LGTM

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