feat: add test_longreadonly_alternatives snapshot#1028
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dialvarezs
requested review from
d4straub,
jfy133,
muabnezor and
prototaxites
as code owners
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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. |
prototaxites
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prototaxites
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Hi @dialvarezs, this looks really good! I mostly just have a comment about fixing the Flye CPUs - otherwise, this looks really comprehensive.
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| process { | ||
| withName: FLYE { | ||
| cpus = 1 |
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Is this for reproducibility? Is it worth adding a parameter for this to force a fix as with Spades/Megahit?
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Yes, I had to set cpus to 1 because assembly results were not stable.
For consistency I think it would make sense to add an option for that and document it in the reproducibility section. But going to leave it for another PR to keep the scope of this PR.
jfy133
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jfy133
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Just a question but otherwise looks good!
| "MaxBin2 produced unbinned/discarded output: ${maxbin2_unbins.size() > 0}", | ||
| "MetaBAT2 produced classified or unclassified output: ${metabat2_bins.size() + metabat2_unbins.size() > 0}", | ||
| // Summary row count checks | ||
| "Bin summary non-empty: ${bin_summary.csv(sep: '\t').rowCount > 0}", |
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Questio nagain from the previous PR, is there a reason why you don't check for > 1, to make sure you have more than just the header?
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nft-csv doesn't count the header, so this is actually checking for at least one data row.
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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).