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Merged
LilyAnderssonLee merged 4 commits into from
Oct 3, 2025
Merged

Enable runs for PACBIO_SMRT #653

LilyAnderssonLee merged 4 commits into from
Oct 3, 2025

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@LilyAnderssonLee
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@LilyAnderssonLee LilyAnderssonLee commented Sep 26, 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/taxprofiler branch on the nf-core/test-datasets repository.
  • 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).

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github-actions bot commented Sep 26, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 267c893

+| ✅ 291 tests passed       |+
!| ❗  18 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • local_component_structure - kraken2_standard_report.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - krona_cleanup.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - visualization_krona.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - standardisation_profiles.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - longread_filtering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - nonpareil.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - shortread_hostremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-10-03 09:54:44

@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Sep 26, 2025
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jfy133
jfy133 approved these changes Sep 29, 2025
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LGTM, Only other question is if it's been tested, or do you plan to ask the person who reported the issue to test it?

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LilyAnderssonLee commented Sep 29, 2025 •
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I have tested locally with this samplesheet.csv and it worked. Please also check the MultiQC report. Feel free to test it.
samplesheet.csv
multiqc_report.html.zip

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jfy133 commented Sep 29, 2025

OK nice! The MultiQC report doesn't load to me (I think you were too fast with commenting),

But I trust you - you can merge in!

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LilyAnderssonLee commented Sep 29, 2025

You could check MultiQC report now. Please double check. I might missed some parts.

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jfy133 commented Oct 3, 2025

Based on the MQC report: hrm, did you have a FASTQ or FASTA file for your test?

If the former, I'm wondering if we do need to at least send PacBio FASTQ files at least for running the initial FASTQC/FALCO, it confused me when I didn't see it

Ohterwise it still looks good :)

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LilyAnderssonLee commented Oct 3, 2025

Very good point. I tested with the FASTQ files. Updated with your suggestion:
image

The standard format of pacbio data is bam, so users need to convert bam file into fastq before running the pipeline.

@LilyAnderssonLee LilyAnderssonLee merged commit 9480f7d into dev Oct 3, 2025
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@LilyAnderssonLee LilyAnderssonLee deleted the pacbio branch October 3, 2025 11:38
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jfy133 commented Oct 3, 2025

Thank you @LilyAnderssonLee !

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@jfy133 jfy133 jfy133 approved these changes

@sofstam sofstam Awaiting requested review from sofstam sofstam is a code owner

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