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Each host removal route (bowtie2/minimap2, deacon, hostile) should save both short- and long-read output to analysis_ready_fastqs, and deacon should keep separate outputs per run (nf-core#775).
- SAMTOOLS_FASTQ: match *_other.fastq.gz, the long reads passed on downstream - HOSTILE_CLEAN_SHORTREADS/LONGREADS and DEACON_FILTER: publish to analysis_ready_fastqs - DEACON_FILTER: name outputs <sample>_<run> so runs of one sample don't overwrite each other Fixes nf-core#775
nf-core lint (nf_test_content) wants every pipeline test to cover versions.yml. The hostile test checks the file exists, as it has no snapshot.
Also restore ro-crate-metadata.json, which a local lint run had reformatted.
stev004
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LilyAnderssonLee,
jfy133 and
sofstam
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October 24, 2026 05:53
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 4.1.0. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
melon names its output after the input file, and sylph's report includes it, so the run accession now shows up there too.
jfy133
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Oct 24, 2026
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Conceptually fix makes sense, just have some comments around the fix itself
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| ### `Fixed` | ||
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| - [#782](https://github.com/nf-core/taxprofiler/pull/782) Fixed empty `analysis_ready_fastqs` after host removal with minimap2, hostile or deacon, and deacon outputs of runs from the same sample overwriting each other (by @stev004) |
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Suggested change
| - [#782](https://github.com/nf-core/taxprofiler/pull/782) Fixed empty `analysis_ready_fastqs` after host removal with minimap2, hostile or deacon, and deacon outputs of runs from the same sample overwriting each other (by @stev004) | |
| - [#782](https://github.com/nf-core/taxprofiler/pull/782) Fixed empty `analysis_ready_fastqs/` after host removal with minimap2, hostile or deacon, and deacon outputs of runs from the same sample overwriting each other (by @stev004) |
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| nextflow_pipeline { | |||
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| name "Test analysis-ready FASTQs after host removal" | |||
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I don't think we need a whole separate test for this, do not already have a test including this step turned on in one of the other profiles? 🤔
Or if indeed do not have any existing test testing this, can we merge this test with one of the existing ones?
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Good point. I've dropped the separate test and turned it on in the existing bowtie2/minimap2, hostile and deacon tests instead.
One thing I noticed: with run merging on, the per-run reads end up in there next to the merged ones. Looks like a separate bug, so I can open an issue for it.
| test("-profile test_minimal --save_analysis_ready_fastqs - bowtie2 and minimap2 host removal") { | ||
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If this test is restrained ,we actually specify all params in a dedicated netzflow config file under test/ to have the ability to run the test configuration without nf-test itself. See the other tests for examples
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Not needed now the separate test is gone.
Instead of a separate test, turn on save_analysis_ready_fastqs in test_falcobbduk (bowtie2/minimap2), test_alternativepreprocessing (hostile) and test_fastpnonpareilkrakenuniq (deacon). Also take the CHANGELOG wording from review.
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Will do it during the week :) Thanks for the quick review @jfy133 |
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Closes #775.
With host removal on,
--save_analysis_ready_fastqsmissed the host-removed reads:*_other.fastq.gz, but the pattern was*.fq.gzanalysis_ready_fastqsentry at allI've added the missing entries and fixed the pattern. DEACON_FILTER now also uses
${meta.id}_${meta.run_accession}as its prefix, like the other host removal steps, because runs from the same sample were overwriting each other indeacon/filter/. That also changes melon's output names and sylph's report for single-run samples, so thedefaultsnapshot is updated too.To test it,
save_analysis_ready_fastqsis now on intest_falcobbduk(bowtie2 and minimap2),test_alternativepreprocessing(hostile) andtest_fastpnonpareilkrakenuniq(deacon). I got the new file names for bowtie2/minimap2 and deacon from local runs. Hostile runs out of memory on my machine, so I worked out its names from how prinseq++ and hostile name their outputs, and CI will confirm those.PR checklist
nf-core pipelines lint).docs/output.mdis updated.CHANGELOG.mdis updated.This was AI-assisted (Claude Code). I've gone through all the changes and test runs myself and understand them.
🤖 Generated with Claude Code