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add Prokka to MultiQC #295

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merged 6 commits into from
Jul 19, 2023
Merged

add Prokka to MultiQC #295

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ff839b9
add Prokka to MultiQC
louperelo Jul 13, 2023
7a69688
[automated] Fix linting with Prettier
nf-core-bot Jul 14, 2023
e2a95fd
update changelog
louperelo Jul 14, 2023
746718a
Merge branch 'dev' into prokka_mqc
louperelo Jul 14, 2023
53cd340
[automated] Fix linting with Prettier
nf-core-bot Jul 14, 2023
74b59d0
Apply suggestions from code review
louperelo Jul 19, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [#290](https://github.com/nf-core/funcscan/pull/290) Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133)

- [#295](https://github.com/nf-core/funcscan/pull/295) Add Prokka to MultiQC output (by @louperelo)

### `Fixed`

- [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)

### `Dependencies`

### `Deprecated`
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3 changes: 3 additions & 0 deletions assets/multiqc_config.yml
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Expand Up @@ -15,3 +15,6 @@ export_plots: true
custom_logo: "nf-core-funcscan_logo_flat_light.png"
custom_logo_url: https://nf-co.re/funcscan
custom_logo_title: "nf-core/funcscan"

## Tool specific configuration
prokka_fn_snames: True
1 change: 1 addition & 0 deletions workflows/funcscan.nf
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Expand Up @@ -282,6 +282,7 @@ workflow FUNCSCAN {
ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
if(params.annotation_tool=='prokka'){ch_multiqc_files = ch_multiqc_files.mix(PROKKA.out.txt.collect{it[1]}.ifEmpty([]))}
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MULTIQC (
ch_multiqc_files.collect(),
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