From 1afe7cbbbc95a8ef4e57030de4813621775720e9 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 16 May 2024 15:24:27 +0200 Subject: [PATCH] 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 ca644cc5..4decf454 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) } // @@ -474,8 +474,8 @@ 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([]))