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feat: Add bakta to run modules in multiqc #543

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739b16b
feat: Add bakta to run modules in multiqc
jvfe Aug 15, 2026
6bb5c11
chore: Update changelog
jvfe Aug 15, 2026
faa8103
fix: Revert conditional change
jvfe Aug 21, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#543](https://github.com/nf-core/funcscan/pull/543) Added Bakta output support to MultiQC report by adding `bakta` to `run_modules` in `assets/multiqc_config.yml` and aligning the MultiQC file mixing condition with the ANNOTATION subworkflow condition. (by @jvfe)

### `Fixed`

- [#538](https://github.com/nf-core/funcscan/pull/538) Fixed sequence validation to handle `NaN` values in DRAMP database download. (by @hindrek)
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4 changes: 4 additions & 0 deletions assets/multiqc_config.yml
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Expand Up @@ -10,11 +10,14 @@ report_section_order:

run_modules:
- prokka
- bakta
- custom_content

table_columns_visible:
Prokka:
organism: false
Bakta:
organism: false

export_plots: true

Expand All @@ -26,3 +29,4 @@ custom_logo_title: "nf-core/funcscan"

## Tool specific configuration
prokka_fn_snames: true
bakta_fn_snames: true
4 changes: 2 additions & 2 deletions workflows/funcscan.nf
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Expand Up @@ -433,8 +433,8 @@ workflow FUNCSCAN {
def ch_methods_description = channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml', sort: true))

if ((params.run_arg_screening && !params.arg_skip_deeparg) || (params.run_amp_screening && (params.amp_run_hmmsearch || !params.amp_skip_amplify || !params.amp_skip_ampir)) || params.run_bgc_screening) {
ch_multiqc_files = ch_multiqc_files.mix(ANNOTATION.out.multiqc_files.collect { it[1] })
if ((params.run_arg_screening && !params.arg_skip_deeparg) || params.run_amp_screening || params.run_bgc_screening || params.run_cazyme_screening) {
ch_multiqc_files = ch_multiqc_files.mix(ANNOTATION.out.multiqc_files)
}

MULTIQC(
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