Gecco convert #506

SkyLexS · 2025-11-11T12:47:51Z

PR checklist

Release PR for 3.0.0

jfy133

Very good first PR @SkyLexS , well done

The code itself looks good, however I've left comments to improve a couple of places.

You will also need to update:

CHANGELOG.md: describe you changes for the next release's announcement
output.md : to describe the differnet output files we should see in the gecco/ results directory (presumable)
README.md: to add yourself as a contributor

subworkflows/local/bgc.nf

jfy133 · 2025-11-11T13:11:40Z

nextflow_schema.json

+                    "type": "boolean",
+                    "default": false,
+                    "description": "Enable conversion of contig FASTA files to GECCO-compatible format.",
+                    "help_text": "GECCO requires contig FASTA files to be in a specific format. Enabling this option will convert the input FASTA files to the required format before running GECCO.\n\n> Modifies tool parameter(s):\n> - gecco convert: `--enable`"


Unless I misunderstand #450 , this phrasing is confusing to me.

I thought (and the code says) you run GECCO_CONVERT after GECCO_RUN to convert the files to other formats for downstream processes, not to convert input files into one that GECCO accepts.

Could you please reprhase or re-explain to me the purposes of the GECCO_CONVERT module (I'm not that familiar1)

jfy133 · 2025-11-11T13:12:32Z

nextflow_schema.json

+                    "type": "string",
+                    "default": "clusters",
+                    "description": "Mode for converting contig FASTA files for GECCO.",
+                    "help_text": "Select the mode for converting contig FASTA files. 'default' uses standard conversion settings, while 'custom' allows for user-defined parameters.\n\n> Modifies tool parameter(s):\n> - gecco convert: `--mode`"


If there are different options, please use the pipe-separated list to indicate this (in the nf-core pipelines schema build interface, if you press the gear next to the parameter entry you should see the box to enter it in.

What does custom mean here though - where does a user specify the additional paramaeters?

docs/output.md

nf-core-bot · 2025-11-19T22:33:26Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.4.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

jfy133

Looking very close to being done @SkyLexS !

May seem like lots of comments but it's mostly replacing the parameter names to make sure they follow the same structure as the other pipeline parameters :)

jfy133 · 2025-11-25T16:59:05Z

docs/output.md

 [deepBGC](https://github.com/Merck/deepbgc) detects BGCs in bacterial and fungal genomes using deep learning. DeepBGC employs a Bidirectional Long Short-Term Memory Recurrent Neural Network and a word2vec-like vector embedding of Pfam protein domains. Product class and activity of detected BGCs is predicted using a Random Forest classifier.

-#### GECCO
+#### GECCO & GECCO CONVERT


Suggested change

#### GECCO & GECCO CONVERT

#### GECCO

They are from the same package so should be fine as just GECCO

jfy133 · 2025-11-25T17:01:09Z

nextflow.config

+    run_gecco_convert                               = false
+    gecco_convert_mode                              = 'clusters'
+    gecco_convert_format                            = 'gff'


Suggested change

run_gecco_convert = false

gecco_convert_mode = 'clusters'

gecco_convert_format = 'gff'

bgc_gecco_runconvert = false

bgc_gecco_convertmode = 'clusters'

bgc_gecco_convertformat = 'gff'

For consistency with the rest of the parameter system.

Make sure to update the parameters throughout the code base too

jfy133 · 2025-11-25T17:01:46Z

docs/output.md

+  - `*.region*.gbk`: Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE
+  - `*.faa`: Amino-acid FASTA converted GenBank files of all the proteins in a cluster
+  - `*.fna`:Nucleotide sequence FASTA converted GenBank files from the cluster
+  **ONLY IF --run_gecco_convert**


Suggested change

**ONLY IF --run_gecco_convert**

- **GECCO CONVERT**

- `*.gff`: GFF3 converted cluster tables containing the position and metadata for all the predicted clusters (only if `--bgc_gecco_runconvert`)

- `*.region*.gbk`: Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE (only if `--bgc_gecco_runconvert`)

- `*.faa`: Amino-acid FASTA converted GenBank files of all the proteins in a cluster (only if `--bgc_gecco_runconvert`)

- `*.fna`:Nucleotide sequence FASTA converted GenBank files from the cluster (only if `--bgc_gecco_runconvert`)

For the change of parameter name, see comment below.

jfy133 · 2025-11-25T17:03:00Z

docs/output.md


+[GECCO CONVERT] (https://gecco.embl.de) is an option in gecco which does file conversion into formats like GFF3, GenBank, or FASTA for further analysis.


Suggested change

[GECCO CONVERT] (https://gecco.embl.de) is an option in gecco which does file conversion into formats like GFF3, GenBank, or FASTA for further analysis.

The additional GFF3, GenBank, or FASTA files from `--bgc_gecco_runconvert`, can be useful for additional further analysis of the BGC hits.

jfy133 · 2025-11-25T17:05:25Z

CHANGELOG.md

 ### `Added`

 - [#500](https://github.com/nf-core/funcscan/pull/500) Updated pipeline template to nf-core/tools version 3.4.1 (by @jfy133)
+- [#506](https://github.com/nf-core/funcscan/pull/506) Gecco convert (by @SkyLexS)


Suggested change

- [#506](https://github.com/nf-core/funcscan/pull/506) Gecco convert (by @SkyLexS)

- [#506](https://github.com/nf-core/funcscan/pull/506) Added support GECCO convert for generation of additional files useful for downstream analysis (by @SkyLexS)

jfy133 · 2025-11-25T17:07:03Z

nextflow_schema.json

+                    "description": "Enable GECCO file conversion.",
+                    "help_text": "Converts GECCO output into formats like GFF3, GenBank, or FASTA for further analysis. Modifies tool parameter - gecco convert: `--run_gecco_convert true`"
+                },
+                "gecco_convert_mode": {


Suggested change

"gecco_convert_mode": {

"bgc_gecco_convertmode": {

jfy133 · 2025-11-25T17:07:23Z

nextflow_schema.json

+                    "description": "Select conversion mode.",
+                    "help_text": "Either clusters or gbk folder output, depending on what is reformatted. Modifies tool parameter: - gecco convert: `--gecco_convert_mode `"
+                },
+                "gecco_convert_format": {


Suggested change

"gecco_convert_format": {

"bgc_gecco_convertformat": {

jfy133 · 2025-11-25T17:07:40Z

nextflow_schema.json

+                "gecco_convert_mode": {
+                    "type": "string",
+                    "default": "clusters",
+                    "description": "Select conversion mode.",


Suggested change

"description": "Select conversion mode.",

"description": "Specify conversion mode for GECCO convert.",

jfy133 · 2025-11-25T17:07:58Z

nextflow_schema.json

+                "gecco_convert_format": {
+                    "type": "string",
+                    "default": "gff",
+                    "description": "Set output format.",


Suggested change

"description": "Set output format.",

"description": "Specify output format for GECCO convert.",

jfy133 · 2025-11-25T17:08:41Z

nextflow_schema.json

+                    "type": "string",
+                    "default": "gff",
+                    "description": "Set output format.",
+                    "help_text": "Choose output format: 'gff', 'fasta', or 'genbank'. Modifies tool parameter: - gecco convert: `--gecco_convert_format`"


My previous comment from the first review has not been addressed yet #506 (comment)

If you need more guidance just ask on Slack :)

jfy133 · 2025-12-01T08:43:52Z

@SkyLexS what's the status on this, it it ready for re-review? I see one of the commetns on output.md wasn't addressed yet

jfy133

I think the last thing missing now is including gecco convert in one of the test profiles, and have the corresponding tests/* nf-test and snapshot files updated accordingly!

And then I think we are ready!

docs/output.md

jfy133 · 2025-12-03T12:46:29Z

nextflow_schema.json

            "fa_icon": "fas fa-angle-double-right"
        },
+
+        "bgc_gecco_convert": {


Sorry I missed this in the first review, these three should go within the exsiting bgc_gecco section, not in it's own

jfy133

Hi @SkyLexS ! This is looking very good now, however apparently my crappy couple of months work wise meant I've not been doing a very good at doing comprehensive reviews - which I feel very guilty about. Sorry about this.

So you don't have to go through another rigamole of reviews, I'm just going to make the changes directly myself so you can see what else was missing (mostly related to the tests).

So what you've done so far is high quality I just forgot a few extra things mostly nf-core specific that also need to be added (but this isn't your fault).

Self notes:

~~Missing explicit capture of output files in modules.config~~ Didn't need

In addition, while you have updated the test_*.configs, you've not yet updated the nf-test assertions (in tests/*.nf.test) and then run nf-test test --tag <test_name> --profile +docker --update-snapshots to update snapshots themselves

nextflow_schema.json

subworkflows/local/bgc.nf

…k of invalid combinations

…gecco_convert_dis

jfy133

So in my previous few commits

test_*config: I had to change the samplesheets used in the BGC tests to actually produce sufficient BGC hits for GECCO convert to actually run
utils_nfcore...: I added additional input validation checks so a gecco convert format cannot be requested with the wrong mode
bgc.nf: Added the versions mixing
*.nf.test *.snap Added new assertions to the test files and updated their snapshots accordingly
nextflow_schema.json: improved the descriptions, and used the correct enums

Please review my changes @SkyLexS and @amizeranschi , and if you're happy I think we are NOW ready to merge 🎉 :D

conf/modules.config

jfy133 · 2025-12-21T11:44:39Z

Ok, I think I will need to update the bakta module. It was working locally at least and given it's failing on database downloading is not caused by the changes in this PR, so will merge.

Thanks for all the hard work @SkyLexS /@Gbs08407 /@amizeranschi !

jfy133 and others added 9 commits October 4, 2025 20:56

Merge pull request nf-core#497 from nf-core/dev

fa9db01

Release PR for 3.0.0

Integrating gecco_convert into funcscan

5a2afa6

Rearranging the code

0012b8a

fixing

518a7a1

fixing typos

f636670

fixing some error

0fd918f

polishing the integration

a1bcca7

fixing warnings

8e4f163

Merge branch 'nf-core:master' into gecco_convert_dis

f5ff043

SkyLexS self-assigned this Nov 11, 2025

SkyLexS requested a review from jfy133 as a code owner November 11, 2025 12:47

SkyLexS added the enhancement Improvement for existing functionality label Nov 11, 2025

SkyLexS requested review from Darcy220606 and jasmezz as code owners November 11, 2025 12:47

SkyLexS added the first-timers-only Good for newcomers label Nov 11, 2025

jfy133 reviewed Nov 11, 2025

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SkyLexS added 3 commits November 11, 2025 17:02

Update for the schema and the function calling

686b2ff

updated output.md

ed55447

added tests

242592d

jfy133 reviewed Nov 18, 2025

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docs/output.md Outdated Show resolved Hide resolved

fixed allOf section for gecco convert

a5d0119

SkyLexS added 2 commits November 23, 2025 14:35

redid the output to include gecco convert

ecfdfd3

updated changelog.md and readme.md

81b1160

jfy133 reviewed Nov 25, 2025

View reviewed changes

SkyLexS added 3 commits November 25, 2025 20:40

implemented the changes

43a2964

removing the unwanted code in the modules config

2e62888

fixing lint

c9244b7

removed unwanted comment

000326b

SkyLexS requested a review from jfy133 December 1, 2025 18:06

jfy133 reviewed Dec 3, 2025

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SkyLexS added 4 commits December 4, 2025 08:44

Implemented schema modification

d6a9dcb

Linting

8104d87

updated test configs

ecd72c7

Linting

fb9a4ff

amizeranschi requested a review from jfy133 December 8, 2025 17:43

jfy133 linked an issue Dec 9, 2025 that may be closed by this pull request

Enable GECCO optional features for integration with other tools #450

Open

jfy133 reviewed Dec 17, 2025

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jfy133 added 6 commits December 17, 2025 11:35

Update docs/output.md

df1e3ac

Fix convert format options to match gecco itself, add validation chec…

a9a561a

…k of invalid combinations

Update tests

47a9254

Merge branch 'gecco_convert_dis' of github.com:SkyLexS/funcscan into …

e789973

…gecco_convert_dis

Update BAKTA test with final test profile

1ec8cee

Merge branch 'dev' into gecco_convert_dis

a06d281

jfy133 reviewed Dec 18, 2025

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Update conf/modules.config

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jfy133 merged commit b0c0f23 into nf-core:dev Dec 21, 2025
121 of 135 checks passed

-  **ONLY IF --run_gecco_convert**
+  - **GECCO CONVERT**
+  - `*.gff`: GFF3 converted cluster tables containing the position and metadata for all the predicted clusters (only if `--bgc_gecco_runconvert`)
+  - `*.region*.gbk`: Converted and aliased GenBank files so that they can be loaded by BiG-SLiCE (only if `--bgc_gecco_runconvert`)
+  - `*.faa`: Amino-acid FASTA converted GenBank files of all the proteins in a cluster (only if `--bgc_gecco_runconvert`)
+  - `*.fna`:Nucleotide sequence FASTA converted GenBank files from the cluster (only if `--bgc_gecco_runconvert`)


		[GECCO CONVERT] (https://gecco.embl.de) is an option in gecco which does file conversion into formats like GFF3, GenBank, or FASTA for further analysis.


	[GECCO CONVERT] (https://gecco.embl.de) is an option in gecco which does file conversion into formats like GFF3, GenBank, or FASTA for further analysis.
	The additional GFF3, GenBank, or FASTA files from `--bgc_gecco_runconvert`, can be useful for additional further analysis of the BGC hits.

	- [#506](https://github.com/nf-core/funcscan/pull/506) Gecco convert (by @SkyLexS)
	- [#506](https://github.com/nf-core/funcscan/pull/506) Added support GECCO convert for generation of additional files useful for downstream analysis (by @SkyLexS)

	"description": "Select conversion mode.",
	"description": "Specify conversion mode for GECCO convert.",

	"description": "Set output format.",
	"description": "Specify output format for GECCO convert.",

Gecco convert #506

Gecco convert #506

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SkyLexS commented Nov 11, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core-bot commented Nov 19, 2025

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jfy133 commented Dec 1, 2025

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jfy133 commented Dec 21, 2025

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