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Update porechop/abi to patched version to not result in duplicated reads#854

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jfy133 merged 3 commits intodevfrom
porechop-update
Sep 3, 2025
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Update porechop/abi to patched version to not result in duplicated reads#854
jfy133 merged 3 commits intodevfrom
porechop-update

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@jfy133 jfy133 commented Aug 25, 2025 •
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nf-core/mag pull request

To close #840

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/mag 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 Aug 25, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 266f271

+| ✅ 363 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • 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!

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-09-03 10:17:21

dialvarezs
dialvarezs approved these changes Aug 25, 2025
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LGTM!

dialvarezs
dialvarezs reviewed Aug 25, 2025
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Comment thread subworkflows/local/preprocessing_longread/main.nf
Comment on lines +121 to +123
if (!(val_skip_qc && !(params.host_fasta || params.host_genome))) {
if (!(params.skip_adapter_trimming && params.skip_longread_filtering && params.keep_lambda && !(params.host_fasta || params.host_genome))) {
NANOPLOT_FILTERED(
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@dialvarezs dialvarezs Aug 25, 2025 •
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[non-blocking] Looking at this a second time, I feel a bit more unconfortable with this nested negation. Can we try to simplify it? I know the logic is described in the comment, but the code should be easy to follow too.

Maybe we can define some auxiliary variables to make it easier to read:

def _has_host_data = params.host_fasta || params.host_genome
def _skip_all_processing = params.skip_adapter_trimming && params.skip_longread_filtering && params.keep_lambda

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@jfy133 jfy133 Aug 26, 2025

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I like the idea! Maybe youcan make an issue for a future release?

@dialvarezs dialvarezs mentioned this pull request Aug 26, 2025
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jfy133
jfy133 commented Sep 3, 2025
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Comment thread CHANGELOG.md Outdated
@jfy133 jfy133 merged commit a8087b6 into dev Sep 3, 2025
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@dialvarezs dialvarezs deleted the porechop-update branch November 21, 2025 11:36
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@dialvarezs dialvarezs dialvarezs approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

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

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

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