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Add nf-test: test_falcobbduk#698

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jfy133 merged 6 commits intodevfrom
nftest-bbduk
Mar 18, 2026
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Add nf-test: test_falcobbduk#698
jfy133 merged 6 commits intodevfrom
nftest-bbduk

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@jfy133 jfy133 commented Mar 5, 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
  • 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 Mar 5, 2026

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/taxprofiler master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/taxprofiler dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@jfy133 jfy133 changed the base branch from master to dev March 5, 2026 08:34
@github-actions github-actions bot added the size/l label Mar 5, 2026
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github-actions bot commented Mar 5, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b9a09b6

+| ✅ 302 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  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 - shortread_preprocessing.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 - longread_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 - shortread_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/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 - longread_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 - shortread_hostremoval.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 - profiling.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_complexityfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-15 05:40:58

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jfy133 commented Mar 5, 2026

@nf-core-bot fix linting

sofstam
sofstam reviewed Mar 11, 2026
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A few comments.

tests/test_falcobbduk.nf.test

then {
def stable_name_all = getAllFilesFromDir(params.outdir, relative: true , includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
// bbduk: partly unstable files, see custom assertions
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Since for bbduk there are partly unstable files, shall the stable_content_bbduk be defined too? This is how I did for the default.nf.test and I am wondering what would be the best strategy.

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@jfy133 jfy133 Mar 14, 2026

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Partly in this case I mean the files themselves are partly unstable (not the entire file is completely non-deterministic) - not that some files are stable and none are not.

In this case both teh log and FASTQ files vary slightly.

tests/test_falcobbduk.nf.test
{ assert snapshot (
stable_content_falco,
file("$outputDir/falco/processed/2612_ERR5766176_1.fastp.fastq.gz_fastqc_data.txt").getName() + " contains string '151 0.177308': " + file("$outputDir/falco/processed/2612_ERR5766176_1.fastp.fastq.gz_fastqc_data.txt").text.contains("151 0.177308"),
file("$outputDir/falco/processed/2612_ERR5766176_2.fastp.fastq.gz_fastqc_data.txt").getName() + " contains string '151 0.173329': " + file("$outputDir/falco/processed/2612_ERR5766176_2.fastp.fastq.gz_fastqc_data.txt").text.contains("151 0.173329"),
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@sofstam sofstam Mar 11, 2026

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Same here

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@jfy133 jfy133 Mar 14, 2026 •
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As above, each file is changing, the strings being checked against are not consistent across all files

tests/test_falcobbduk.nf.test
},

// kaiju
{ assert snapshot (
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@sofstam sofstam Mar 11, 2026

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Here as well.

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@jfy133 jfy133 Mar 14, 2026

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And above again :)

@jfy133 jfy133 requested a review from sofstam March 14, 2026 20:21
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jfy133 commented Mar 18, 2026

Thanks @sofstam !

@jfy133 jfy133 merged commit 96d561b into dev Mar 18, 2026
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@jfy133 jfy133 deleted the nftest-bbduk branch March 18, 2026 10:39
@jfy133 jfy133 restored the nftest-bbduk branch March 18, 2026 10:39
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@sofstam sofstam sofstam approved these changes

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

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