added prefix to krona html results

Daniel-VM · Aug 30, 2024 · e4e6f16 · e4e6f16
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diff --git 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.
diff --git 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