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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: 3.3.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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jfy133
commented
Apr 24, 2026
jasmezz
approved these changes
Apr 29, 2026
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| title: 'nf-core/funcscan: A Nextflow pipeline to identify the biosynthetic potential and resistome of bacterial (meta)genomes' | |||
| title: "nf-core/funcscan: A Nextflow pipeline to identify the biosynthetic potential and resistome of bacterial (meta)genomes" | |||
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Why double quotes, because it's normal text? We can have double, but the provided example in the joss documentation has single quotes as well as all publications I've checked. (It makes no difference when I render it, though.)
| : Comparison of nf-core/funcscan with other related pipelines for ARG, AMP, and BGC discovery. Parentheses indicate either unspecific gene screening or partly fulfilled criteria. \label{tab:pipelines} | ||
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| # Software design | ||
| # Workflow overview |
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Officially, the paper should contain a "Software design" section, but it seems not to be strict. Other papers have it named "Workflow overview" as well. I agree here; it fits better to a Nextflow pipeline.
| (3), the results of all tools for each gene category are aggregated and saved in a human- and machine-readable tabular format.\label{fig:workflow}](figure1.png) | ||
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| ## Input pre-processing and open reading frame annotation | ||
| ## Input preprocessing and open reading frame annotation |
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Okay I am confused when to use hyphen or not :D Below you prefer it as "sample-sheet" and "pre-annotated". I assume joining domain specific terms with hyphen, and common words with no hyphen is preferred.
Co-authored-by: Jasmin Frangenberg <73216762+jasmezz@users.noreply.github.com>
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@nf-core-bot fix linting |
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Thank you for thorough reading/suggestions/comments @jfy133! 🚀 I'll merge and work on the remaining todos. |
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More general comments:
Maybe use:
As guides to work out what level of detail you need to go in. I think some sections are a bit too wordy for JOSS.