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fix samples reported of prokka/bakta in multiqc report #134

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merged 3 commits into from
May 17, 2024
Merged

fix samples reported of prokka/bakta in multiqc report #134

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e8ddcc2
fix samples reported in prokka/bakta multiqc report
Daniel-VM May 16, 2024
647066f
update changelog #134
Daniel-VM May 16, 2024
495debc
add multiqc report generic method to name samples
Daniel-VM May 17, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#134](https://github.com/nf-core/bacass/pull/134) - Fixed samples reported of prokka/bakta in multiqc report.

- [#125](https://github.com/nf-core/bacass/pull/125) - Fixed conflicting settings in save_trimmed_fail parameter.

### `Dependencies`
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3 changes: 3 additions & 0 deletions assets/multiqc_config.yml
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Expand Up @@ -13,3 +13,6 @@ report_section_order:
export_plots: true

disable_version_detection: true
use_filename_as_sample_name:
- prokka
- bakta
8 changes: 4 additions & 4 deletions workflows/bacass.nf
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Expand Up @@ -413,7 +413,7 @@ workflow BACASS {
[],
[]
)
ch_prokka_txt_multiqc = PROKKA.out.txt.collect()
ch_prokka_txt_multiqc = PROKKA.out.txt.map{ meta, prokka_txt -> [ prokka_txt ]}
ch_versions = ch_versions.mix(PROKKA.out.versions)
}

Expand All @@ -432,7 +432,7 @@ workflow BACASS {
params.baktadb,
params.baktadb_download
)
ch_bakta_txt_multiqc = BAKTA_DBDOWNLOAD_RUN.out.bakta_txt_multiqc.collect()
ch_bakta_txt_multiqc = BAKTA_DBDOWNLOAD_RUN.out.bakta_txt_multiqc.map{ meta, bakta_txt -> [ bakta_txt ]}
ch_versions = ch_versions.mix(BAKTA_DBDOWNLOAD_RUN.out.versions)
}
//
Expand Down Expand Up @@ -478,8 +478,8 @@ workflow BACASS {
ch_multiqc_files = ch_multiqc_files.mix(ch_kraken_short_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_kraken_long_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_quast_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_prokka_txt_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_bakta_txt_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_prokka_txt_multiqc.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_bakta_txt_multiqc.collect().ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_nanoplot_txt_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_porechop_log_multiqc.collect{it[1]}.ifEmpty([]))
ch_multiqc_files = ch_multiqc_files.mix(ch_pycoqc_multiqc.collect{it[1]}.ifEmpty([]))
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