Paper: attempt intro restructuring and word count cutting by jfy133 · Pull Request #542 · nf-core/funcscan

jfy133 · 2026-07-28T09:54:53Z

PR checklist

jasmezz

Thanks for restructuring! ✍️ I'll address the remaining todos next time/asap.

jasmezz · 2026-08-07T09:12:29Z

+However, execution of the multiple bioinformatic tools used in screening analyses remains inefficient due to heterogenous software interfaces, reporting, and formatting of the output files of similar tools, which limits scalability of such analyses.
+
+nf-core/funcscan is a portable and reproducible open source Nextflow bioinformatics pipeline for the screening of microbial functional features from assembled contigs or genomes.
+The pipeline executes up to 13 tools to simultaneously identify antimicrobial peptides, antibiotic resistance genes, biosynthetic gene clusters, carbohydrate-activate enzymes, and perform taxonomic classification of partial or full genomes.


Suggested change

The pipeline executes up to 13 tools to simultaneously identify antimicrobial peptides, antibiotic resistance genes, biosynthetic gene clusters, carbohydrate-activate enzymes, and perform taxonomic classification of partial or full genomes.

The pipeline executes up to 13 tools to simultaneously identify antimicrobial peptides, antibiotic resistance genes, biosynthetic gene clusters, carbohydrate-activate enzymes, and performs taxonomic classification of partial or full genomes.

jasmezz · 2026-08-07T09:16:59Z

+Additionally, each tool often has its own unique output formats, making cross-comparison of results between tools and databases non-trivial, and again requiring inefficient manual postprocessing and inspection.
+
+This necessity for manual execution and postprocessing of heterogenous outputs impacts the discovery of new drugs.
+For example, antibiotics are typically derived from naturally evolved, bacterially-produced, low molecular weight natural products, and the rate of discovery of novel molecules has seen recent plateauing.


Suggested change

For example, antibiotics are typically derived from naturally evolved, bacterially-produced, low molecular weight natural products, and the rate of discovery of novel molecules has seen recent plateauing.

For example, antibiotics are typically derived from naturally evolved, bacterially-produced, low molecular weight natural products, and the discovery rate of novel molecules has seen recent plateauing.

jasmezz · 2026-08-07T09:26:57Z

+<!-- TODO: note, I've removed HT-ARGfinder as it doesn't ave an open source license, to simplify teh table -->
+


Suggested change



Okay, agree!

jasmezz · 2026-08-07T09:30:32Z

+Open reading frames are optionally predicted from the preprocessed sequences by one of four prokaryotic annotation tools: Bakta [@schwengers_bakta_2021], Prodigal [@Hyatt2010-yv], Prokka [@Seemann2014-ee], and Pyrodigal [@Larralde2022-uu].

-## Gene prediction and taxonomic classification
+When required, the pipeline will download required screening-tool databases automatically for the user, and made available for future pipeline runs to minimise runtime and network traffic.


Suggested change

When required, the pipeline will download required screening-tool databases automatically for the user, and made available for future pipeline runs to minimise runtime and network traffic.

When required, the pipeline downloads required screening-tool databases automatically for the user, and makes them available for future pipeline runs to minimise runtime and network traffic.

jasmezz · 2026-08-07T09:31:52Z

- **AMP subworkflow**: ampir [@fingerhut_ampir_2021], AMPlify [@li_models_2023, @li_amplify_2022], hmmsearch, Macrel [@santos-junior_macrel_2020]
- **CAZyme subworkflow**: run_dbCAN [@zheng_dbcan3_2023]
+Users choose to scan genomic sequences in parallel with up-to four dedicated subworkflows for AMPs, ARGs, BGCs, and CGCs.
+User can apply currently up to a total of 13 gene identification tools:


Suggested change

User can apply currently up to a total of 13 gene identification tools:

Up to a total of 13 gene identification tools can be applied:

jasmezz · 2026-08-07T09:36:22Z

- **BGC subworkflow**: antiSMASH, DeepBGC, GECCO [@carroll_accurate_2021], hmmsearch [@eddy_accelerated_2011]
- **AMP subworkflow**: ampir [@fingerhut_ampir_2021], AMPlify [@li_models_2023, @li_amplify_2022], hmmsearch, Macrel [@santos-junior_macrel_2020]
- **CAZyme subworkflow**: run_dbCAN [@zheng_dbcan3_2023]
+Users choose to scan genomic sequences in parallel with up-to four dedicated subworkflows for AMPs, ARGs, BGCs, and CGCs.


Suggested change

Users choose to scan genomic sequences in parallel with up-to four dedicated subworkflows for AMPs, ARGs, BGCs, and CGCs.

Users choose to scan genomic sequences in parallel with up-to four dedicated subworkflows for AMPs, ARGs, BGCs, and CAZymes.

Not CGCs, because we name it CAZymes in the metro workflow and in the list below. Both would be correct though...

jasmezz · 2026-08-07T09:39:58Z

-For AMPs, AMPcombi parses and filters the results of AMP prediction tools, summarises them into single tables, and aligns the AMP hits against a reference AMP database for deeper functional classification.
-We wrote a custom script 'comBGC' for aggregating and standardising the output of the BGC tools.
-These summaries are finally complemented with results from the optional taxonomic classification workflow.
+nf-core/funcscan integrates dedicated tools to aggregate and standardise heterogenous output formats (and gene labels) of multiple screening tools into a single human- and machine-readable tables in CSV format per gene type.


Suggested change

nf-core/funcscan integrates dedicated tools to aggregate and standardise heterogenous output formats (and gene labels) of multiple screening tools into a single human- and machine-readable tables in CSV format per gene type.

nf-core/funcscan integrates dedicated tools to aggregate and standardise heterogenous output formats of multiple screening tools into a single human- and machine-readable tables in CSV format per gene type.

Not (yet) gene labels for all workflows.

jasmezz · 2026-08-07T09:41:18Z

-We wrote a custom script 'comBGC' for aggregating and standardising the output of the BGC tools.
-These summaries are finally complemented with results from the optional taxonomic classification workflow.
+nf-core/funcscan integrates dedicated tools to aggregate and standardise heterogenous output formats (and gene labels) of multiple screening tools into a single human- and machine-readable tables in CSV format per gene type.
+nf-core uses hAMRonization [@mendes_hamronization_2024] for ARGs, AMPcombi [@herbst_actifensin_2025] for AMPs, and a custom script 'comBGC' for BGC tool output.


Suggested change

nf-core uses hAMRonization [@mendes_hamronization_2024] for ARGs, AMPcombi [@herbst_actifensin_2025] for AMPs, and a custom script 'comBGC' for BGC tool output.

nf-core uses hAMRonization [@mendes_hamronization_2024] for ARGs, AMPcombi [@herbst_actifensin_2025] for AMPs, and a custom script 'comBGC' for BGC tool output aggregation.

jasmezz · 2026-08-07T09:42:19Z

-To facilitate configuration and further portability, nf-core provides already centralised configurations for more than 150 institutional computational infrastructures (e.g. HPCs) via the central nf-core/configs repository ([https://nf-co.re/configs](https://nf-co.re/configs)).
-The performance of each pipeline run (including software versions of all applied tools, memory, and CPU usage) is summarised in HTML reports for all steps of all subworkflows for users to estimate future runtime and/or computational resources.
+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 reducing installation problems.


Suggested change

This provides the advantage of isolating the dependencies of all workflows from each other reducing installation problems.

This provides the advantage of isolating the dependencies of all workflows from each other and reducing installation problems.

jasmezz · 2026-08-07T09:44:25Z

+For example, the pipeline received the contribution of the CAZyme screening from community members outside of the original developers.
+User discussions and support on the pipeline and on related research topics occur on the nf-core Slack workspace.
+This illustrates the public interest and proactive efforts from scientific users to use, maintain, and improve the pipeline.
+The pipeline is also already actively being used in research [e.g., @Tighe2024-fq, @Janak2026-ek, Istanbullugil2026-fg, Liepa2026-sw].


Suggested change

The pipeline is also already actively being used in research [e.g., @Tighe2024-fq, @Janak2026-ek, Istanbullugil2026-fg, Liepa2026-sw].

The pipeline is also already actively being used in research [e.g., @Tighe2024-fq, @Janak2026-ek, @Istanbullugil2026-fg, @Liepa2026-sw].

jasmezz · 2026-08-07T09:52:24Z

-In contrast, nf-core/funcscan provides additional AMP screening and the integration of taxonomic classifications for all genes to provide additional ecological context around predicted genes.
-Regarding pipeline stability and reliability, nf-core/funcscan is the only pipeline to implement comprehensive unit tests on both module and pipeline level, using the nf-test [@forer_improving_2024] framework (Table \ref{tab:pipelines}).
-
-| Feature                                 | funcscan | mettannotator | bacannot | HT-ARGfinder | PathoFact | SqueezeMeta | MetaERG | ARGs-OAP |


Todo: How can we adjust the table headers to not overlap in the rendered PDF?

Afaik either horrible fancy latex, or we remove columns.
Or we could put each column as a number, and out in the caption put a legend, e.g. 1. Nf-core/funcscan, 2. Metaannotator

Start re-write and cutdown

e06b12e

jfy133 requested review from Darcy220606 and jasmezz as code owners July 28, 2026 09:54

github-actions Bot added the size/s label Jul 28, 2026

Intro restructured and word count reduced version (1674 words)

8e42610

github-actions Bot added size/xl and removed size/s labels Jul 28, 2026

Merge branch 'paper' into paper-jfycomments-2-intro-redo

425a2a6

jasmezz reviewed Aug 7, 2026

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Paper: attempt intro restructuring and word count cutting - #542

Paper: attempt intro restructuring and word count cutting#542
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	The pipeline executes up to 13 tools to simultaneously identify antimicrobial peptides, antibiotic resistance genes, biosynthetic gene clusters, carbohydrate-activate enzymes, and perform taxonomic classification of partial or full genomes.
	The pipeline executes up to 13 tools to simultaneously identify antimicrobial peptides, antibiotic resistance genes, biosynthetic gene clusters, carbohydrate-activate enzymes, and performs taxonomic classification of partial or full genomes.

	For example, antibiotics are typically derived from naturally evolved, bacterially-produced, low molecular weight natural products, and the rate of discovery of novel molecules has seen recent plateauing.
	For example, antibiotics are typically derived from naturally evolved, bacterially-produced, low molecular weight natural products, and the discovery rate of novel molecules has seen recent plateauing.

		<!-- TODO: note, I've removed HT-ARGfinder as it doesn't ave an open source license, to simplify teh table -->

	When required, the pipeline will download required screening-tool databases automatically for the user, and made available for future pipeline runs to minimise runtime and network traffic.
	When required, the pipeline downloads required screening-tool databases automatically for the user, and makes them available for future pipeline runs to minimise runtime and network traffic.

	User can apply currently up to a total of 13 gene identification tools:
	Up to a total of 13 gene identification tools can be applied:

	Users choose to scan genomic sequences in parallel with up-to four dedicated subworkflows for AMPs, ARGs, BGCs, and CGCs.
	Users choose to scan genomic sequences in parallel with up-to four dedicated subworkflows for AMPs, ARGs, BGCs, and CAZymes.

	nf-core/funcscan integrates dedicated tools to aggregate and standardise heterogenous output formats (and gene labels) of multiple screening tools into a single human- and machine-readable tables in CSV format per gene type.
	nf-core/funcscan integrates dedicated tools to aggregate and standardise heterogenous output formats of multiple screening tools into a single human- and machine-readable tables in CSV format per gene type.

	nf-core uses hAMRonization [@mendes_hamronization_2024] for ARGs, AMPcombi [@herbst_actifensin_2025] for AMPs, and a custom script 'comBGC' for BGC tool output.
	nf-core uses hAMRonization [@mendes_hamronization_2024] for ARGs, AMPcombi [@herbst_actifensin_2025] for AMPs, and a custom script 'comBGC' for BGC tool output aggregation.

	This provides the advantage of isolating the dependencies of all workflows from each other reducing installation problems.
	This provides the advantage of isolating the dependencies of all workflows from each other and reducing installation problems.

	The pipeline is also already actively being used in research [e.g., @Tighe2024-fq, @Janak2026-ek, Istanbullugil2026-fg, Liepa2026-sw].
	The pipeline is also already actively being used in research [e.g., @Tighe2024-fq, @Janak2026-ek, @Istanbullugil2026-fg, @Liepa2026-sw].

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jfy133 commented Jul 28, 2026

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