From 942adad65341e2e3913bfde9556277484b31d5a5 Mon Sep 17 00:00:00 2001 From: victor5lm Date: Tue, 18 Jun 2024 13:12:13 +0200 Subject: [PATCH] Fixed minor mistake in viralrecon results lablog --- .../templates/viralrecon/RESULTS/lablog_viralrecon_results | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bu_isciii/templates/viralrecon/RESULTS/lablog_viralrecon_results b/bu_isciii/templates/viralrecon/RESULTS/lablog_viralrecon_results index d7363bd2..a46faba6 100755 --- a/bu_isciii/templates/viralrecon/RESULTS/lablog_viralrecon_results +++ b/bu_isciii/templates/viralrecon/RESULTS/lablog_viralrecon_results @@ -20,7 +20,7 @@ cat references.tmp | while read in; do cd excel_files_${in}; ln -s ../../../ANAL #Create symbolic links to files that are going to be converted to excel cat references.tmp | while read in; do ln -s ../../ANALYSIS/*/*${in}*/variants/ivar/variants_long_table.csv ${in}_variants_long_table.csv; done -for ref in $(cut -f2 ../../ANALYSIS/samples_ref.txt | sort | uniq); do for organism in $(cut -f3 ../../ANALYSIS/samples_ref.txt | tr '[:lower:]' '[:upper:]' | sort | uniq); do report="../../ANALYSIS/*_${organism}/${ref}_*_viralrecon_mapping/multiqc/multiqc_report.html"; if [ -e $report ]; then ln -s ${report} ./multiqc_report_${ref}_${organism}.html; else echo "Multiqc report not found for reference $reference and organism $organism"; fi; done; done +for ref in $(cut -f2 ../../ANALYSIS/samples_ref.txt | sort | uniq); do for organism in $(cut -f3 ../../ANALYSIS/samples_ref.txt | tr '[:lower:]' '[:upper:]' | sort | uniq); do report="../../ANALYSIS/*_${organism}/${ref}_*_viralrecon_mapping/multiqc/multiqc_report.html"; if [ -e $report ]; then ln -s ${report} ./multiqc_report_${ref}_${organism}.html; else echo "Multiqc report not found for reference $ref and organism $organism"; fi; done; done ln -s ../../ANALYSIS/*_MAG/99-stats/multiqc_report.html ./krona_results.html ln -s ../../ANALYSIS/*/mapping_illumina*.tab ./mapping_illumina.csv ln -s ../../ANALYSIS/*/assembly_stats.csv ./assembly_stats.csv