Update paper.md

[warinner]

Editing of manuscript to reduce length, reduce repetition, and clarify arguments. Also, I made the order of the genes/functions consistent throughout the manuscript to match the title. They now always appear BGC first, then AMPs, then ARGs, then CAZymes/CGCs.

PR checklist

• This comment contains a description of changes (with reason).
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[jasmezz]

Thank you for your improvements and rephrasing, @warinner. Looking good to me, I just added tiny spelling/puntuation fixes.

TODO: Decide whether we strictly follow BE or AE spelling – things like comma or not after "e.g." are not clear, yet (@jfy133).

[warinner]

Hi All, I don't have a preference for British English or American English, but I suggest we do use the Oxford comma to aid with clarity. I find that not using the Oxford comma often leads to confusing ambiguity in lists. Best, Tina

…

On Mon, Sep 14, 2026 at 7:45 AM Jasmin Frangenberg ***@***.***> wrote: ***@***.**** approved this pull request. Thank you for your improvements and rephrasing, @warinner <https://github.com/warinner>. Looking good to me, I just added tiny spelling/puntuation fixes. TODO: Decide whether we strictly follow BE or AE spelling – things like comma or not after "e.g." are not clear, yet ***@***.*** <https://github.com/jfy133>). ------------------------------ In paper/paper.md <#549 (comment)>: > To facilitate efficient results comparison and evaluation, it supports cross-tool output file standardisation and aggregation. # Statement of need -Researchers often use multiple tools to ensure maximum detection sensitivity during genomic screening for potential gene candidates, as each tool uses different search algorithms and microbial metabolite databases. -However, heterogeneous installation, inputs, and execution interfaces of these standalone tools impede scalability, and decrease reproducibility due to user-error when executed manually. -Additionally, individual tools often have their own unique output formats, making cross-comparison of results between tools and databases non-trivial, and again requiring inefficient manual postprocessing and inspection. +Researchers often use multiple tools to maximize detection sensitivity during genomic screening for potential gene candidates, as each tool uses different search algorithms and microbial metabolite databases. +However, heterogeneous installations, inputs, and execution interfaces of these standalone tools impede scalability, and decrease reproducibility due to user-error when executed manually. +Additionally, output formats are not standardized, making cross-comparison of results between tools and databases difficult and requiring inefficient manual postprocessing and inspection. ⬇️ Suggested change -Additionally, output formats are not standardized, making cross-comparison of results between tools and databases difficult and requiring inefficient manual postprocessing and inspection. +Additionally, output formats are not standardised, making cross-comparison of results between tools and databases difficult and requiring inefficient manual postprocessing and inspection. We're using British spelling here consistently. ------------------------------ In paper/paper.md <#549 (comment)>: > -In particular, the main factors that distinguish nf-core/funcscan from the most similar pipeline, mettannotator, are: support for metagenomic assembly input rather than just genomes; automated taxonomic classification of contigs; more tools for ARG screening; support for AMP screening; and confirmed execution on other infrastructure than HPCs. -Genomic functions which nf-core/funcscan does not screen for due to its focus on AMPs, ARGs, and BGCs but mettannotator does are CRISPR arrays, antiphage defence, non-coding RNA, and pseudogenes. +In particular, the main factors that distinguish nf-core/funcscan from the most similar pipeline, mettannotator, are: support for metagenomic assembly input rather than just genomes; automated taxonomic classification of contigs; more tools for ARG screening; support for AMP screening; and confirmed execution on other infrastructure than HPCs. Genomic functions which nf-core/funcscan does not screen for due to its focus on BGCs, AMPs, ARGs, and CAZymes/CGCs but mettannotator does are CRISPR arrays, antiphage defence, non-coding RNA, and pseudogenes. ⬇️ Suggested change -In particular, the main factors that distinguish nf-core/funcscan from the most similar pipeline, mettannotator, are: support for metagenomic assembly input rather than just genomes; automated taxonomic classification of contigs; more tools for ARG screening; support for AMP screening; and confirmed execution on other infrastructure than HPCs. Genomic functions which nf-core/funcscan does not screen for due to its focus on BGCs, AMPs, ARGs, and CAZymes/CGCs but mettannotator does are CRISPR arrays, antiphage defence, non-coding RNA, and pseudogenes. +In particular, the main factors that distinguish nf-core/funcscan from the most similar pipeline, mettannotator, are: support for metagenomic assembly input rather than just genomes; automated taxonomic classification of contigs; more tools for ARG screening; support for AMP screening; and confirmed execution on other infrastructure than HPCs. +Genomic functions which nf-core/funcscan does not screen for due to its focus on BGCs, AMPs, ARGs, and CAZymes/CGCs but mettannotator does are CRISPR arrays, antiphage defence, non-coding RNA, and pseudogenes. ------------------------------ In paper/paper.md <#549 (comment)>: > This enhances ARG annotation by categorising drugs that ARGs confer resistance to. -Secondly, BGCs predicted by antiSMASH and GECCO can be clustered into Gene Cluster Families (GCFs) by BiG-SLiCE ***@***.***_big-slice_2021] to enable comparative analysis of biosynthetic diversity across samples. + ## Reproducibility and scalability All nf-core pipelines utilise software environments [from the Bioconda project, @Gruning2018-vr] or containers [e.g. Docker, Singularity, primarily from the Biocontainers project, @Da_Veiga_Leprevost2017-gl] for each integrated tool. ⬇️ Suggested change -All nf-core pipelines utilise software environments [from the Bioconda project, @Gruning2018-vr] or containers [e.g. Docker, Singularity, primarily from the Biocontainers project, @Da_Veiga_Leprevost2017-gl] for each integrated tool. +All nf-core pipelines utilise software environments [from the Bioconda project, @Gruning2018-vr] or containers [e.g., Docker, Singularity, primarily from the Biocontainers project, @Da_Veiga_Leprevost2017-gl] for each integrated tool. ------------------------------ In paper/paper.md <#549 (comment)>: > ## Reproducibility and scalability All nf-core pipelines utilise software environments [from the Bioconda project, @Gruning2018-vr] or containers [e.g. Docker, Singularity, primarily from the Biocontainers project, @Da_Veiga_Leprevost2017-gl] for each integrated tool. This provides the advantage of isolating the dependencies of all workflows from each other, thereby reducing installation problems. -The pipeline is thus easy to install with few minimum dependencies - Nextflow itself, and one of Nextflow-supported container/software environment management systems. -For further portability, nf-core provides integrated configurations for more than 150 institutional computational infrastructure (e.g. HPCs) via nf-core/configs ([https://nf-co.re/configs](https://nf-co.re/configs)). +The pipeline is thus easy to install with minimal dependencies - Nextflow itself, and one of Nextflow-supported container/software environment management systems. +For further portability, nf-core provides integrated configurations for more than 150 institutional computational infrastructures (e.g. HPCs) via nf-core/configs ([https://nf-co.re/configs](https://nf-co.re/configs)). ⬇️ Suggested change -For further portability, nf-core provides integrated configurations for more than 150 institutional computational infrastructures (e.g. HPCs) via nf-core/configs ([https://nf-co.re/configs](https://nf-co.re/configs)). +For further portability, nf-core provides integrated configurations for more than 150 institutional computational infrastructures (e.g., HPCs) via nf-core/configs ([https://nf-co.re/configs](https://nf-co.re/configs)). — Reply to this email directly, view it on GitHub <#549?email_source=notifications&email_token=ALJIQMNRIWWP3UG6IQSTAXD5O7K6BA5CNFSNUABKM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UKJSXM2LFO4XTKMJZGY4TEOJSGQ22M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#pullrequestreview-5196929245>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALJIQMN2QGMBRUYZSOJXGIT5O7K6BAVCNFSNUABFKJSXA33TNF2G64TZHM2DGNZYGMYTIMJUHNEXG43VMU5TKNBTGY3DQOBZGE3KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/ALJIQMJJ3O7DHMXN7HEJUFL5O7K6BA5CNFSNUABKM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UKJSXM2LFO4XTKMJZGY4TEOJSGQ22M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/ALJIQMPWJJJ2YZDVD22EMAT5O7K6BA5CNFSNUABKM5UWIORPF5TWS5BNNB2WEL2QOVWGYUTFOF2WK43UKJSXM2LFO4XTKMJZGY4TEOJSGQ22M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: <nf-core/funcscan/pull/549/review/5196929245 ***@***.*** com>

[jasmezz]

That sounds good. I'll merge this PR with your improvements so that others have a clean version to read/comment on.