From e8ddcc2b143a8aba1c3003c07301ffbf25bb6568 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 16 May 2024 15:24:27 +0200 Subject: [PATCH 1/3] fix samples reported in prokka/bakta multiqc report --- assets/multiqc_config.yml | 1 + workflows/bacass.nf | 8 ++++---- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 32c030f0..074bbba8 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -13,3 +13,4 @@ report_section_order: export_plots: true disable_version_detection: true +prokka_fn_snames: True diff --git a/workflows/bacass.nf b/workflows/bacass.nf index fa633ce5..076e62c2 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -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) } @@ -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) } // @@ -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([])) From 647066fcc47c9a7e8972bc43e11847f1de5acf48 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 16 May 2024 16:40:55 +0200 Subject: [PATCH 2/3] update changelog #134 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1aad7ad7..3d48b275 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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` From 495debc7f905e69d7714b0b6dcd6bc5c81902f9b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 17 May 2024 09:28:39 +0200 Subject: [PATCH 3/3] add multiqc report generic method to name samples --- assets/multiqc_config.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 074bbba8..e647ad5a 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -13,4 +13,6 @@ report_section_order: export_plots: true disable_version_detection: true -prokka_fn_snames: True +use_filename_as_sample_name: + - prokka + - bakta