From e4e6f16dcd34c476575f03b556fc07eaebf2cd60 Mon Sep 17 00:00:00 2001 From: Dani VM Date: Fri, 30 Aug 2024 15:17:38 +0200 Subject: [PATCH] added prefix to krona html results --- bu_isciii/assets/reports/results/mag.md | 2 +- bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results | 6 +++++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/bu_isciii/assets/reports/results/mag.md b/bu_isciii/assets/reports/results/mag.md index cec03e6b..fa6ea6cb 100644 --- a/bu_isciii/assets/reports/results/mag.md +++ b/bu_isciii/assets/reports/results/mag.md @@ -12,7 +12,7 @@ Here we describe the results from the MAG pipeline for multispecies metagenomic Here we describe the results from the (nf-core/taxprofiler)[https://nf-co.re/taxprofiler/1.1.8] pipeline for multispecies taxonomic classification and profiling of shorgun short- and long-read. * `multiqc_report.html​`: Final HTML report collecting numerical stats from each module executed in this pipeline. -* `krona/*.html`: Interactive HTML files generated by Krona, displaying the results of taxonomic classification. +* `krona/database_*.html`: Interactive HTML files generated by Krona, displaying the results of taxonomic classification for supported tools (Kraken2, Centrifuge, Kaiju, and MALT) > [!WARNING] > Software's versions used in this analysis can be obtained from the `MultiQC` report. \ No newline at end of file diff --git a/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results b/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results index 7c846010..cfb01fa4 100755 --- a/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results +++ b/bu_isciii/templates/mag/RESULTS/lablog_taxprofiler_results @@ -6,5 +6,9 @@ cd $DELIVERY_FOLDER/taxprofiler # Links to reports ln -s ../../../ANALYSIS/*ANALYSIS01_TAXPROFILER/multiqc/multiqc_report.html . -ln -s ../../../ANALYSIS/*ANALYSIS01_TAXPROFILER/krona . +mkdir -p krona +for file in ../../../ANALYSIS/*ANALYSIS01_TAXPROFILER/krona/*.html; do + base=$(basename "$file") + ln -s "../$file" "krona/database_${base}" +done