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I realised the reason why the test didn't work as expected is because I Forgot to supply a reference genome in the test confrig, so it tried to download instead 🤦♂️. I've requested a small test dataset on the hostile reop in the meantime (bede/hostile#70), but also can try again but supplying the small reference genome we use for host removal explicitly and let it be built on the fly, rather than testing download |
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As requested by James I've added a new mitochondrial index to Hostile's storage bucket to facilitate testing requested here |
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Started adding tests thanks to @bede ! I need to clean up the code logic a bit, in particular work out what validation to do (reference genome vs index name etc) |
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FYI I've renamed the human mitochondrial hostile (and deacon indexes) to |
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Just waiting for @bede to address bede/hostile#71 and then this is ready for review! |
Sorted I think, please reopen if not :-) |
sofstam
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Apr 30, 2026
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A few comments and would be nice to update to the latest hostile modules.
| custom_adapters = params.longread_qc_adapterlist ? file(params.longread_qc_adapterlist, checkIfExists: true) : [] | ||
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| if (params.hostremoval_reference) { | ||
| if (params.shortread_hostremoval_tool == 'bowtie2' || params.longread_hostremoval_tool == 'bowtie2') { |
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Do you mean minimap2 for the long read?
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In case helpful, while Hostile does support using Minimap2 for short reads and Bowtie2 for long reads, this is not recommended, and the CLI defaults steer users away from doing this. If this PR is not doing so already, I strongly suggest setting minimap2 as the aligner for long reads and bowtie2 for short reads, stopping users from making bad choices.
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params.longread_hostremoval_tool == 'bowtie2'
I am referring to this statement
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Oops, I think that might be a copy paste error!
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Indeed the longread_hostremoval_tool parameter does not support bowtie2 at all:
taxprofiler/nextflow_schema.json
Line 367 in c2ce5c9
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We apply samtools stats for minimap2. Shall we do the same for hostile?
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Same here for the samtools stats
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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: 3.5.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Transferred from #646
TODO:
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).