From 975b6775f43166706486fccecfb3c22a41e2562a Mon Sep 17 00:00:00 2001 From: Niamh Date: Fri, 7 Aug 2026 11:20:37 +0100 Subject: [PATCH 1/2] adding sample database upload header for upload to svd --- 3_TSO500.sh | 3 +++ 1 file changed, 3 insertions(+) diff --git a/3_TSO500.sh b/3_TSO500.sh index 0df93aa..8b86c32 100755 --- a/3_TSO500.sh +++ b/3_TSO500.sh @@ -91,6 +91,9 @@ for worksheet_id in $(cat worksheets_rna.txt); do else cat analysis/"$sample"/"$sample"_RNA_QC.txt | tail -n1 >> RNA_QC_combined.txt fi + + # make database upload sample list header + echo "sample,worksheet,assay,referral,run,genome_build" > Gathered_Results/Database/samples_database_"$worksheet_id"_RNA.csv # make database upload sample list if [[ "$sample" != NTC* ]]; then From 749a56961f373688b42b87c776e437b3924f0729 Mon Sep 17 00:00:00 2001 From: Niamh Date: Fri, 7 Aug 2026 15:09:23 +0100 Subject: [PATCH 2/2] adding in coverage columns --- 3_TSO500.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/3_TSO500.sh b/3_TSO500.sh index 8b86c32..82e5d1a 100755 --- a/3_TSO500.sh +++ b/3_TSO500.sh @@ -93,7 +93,7 @@ for worksheet_id in $(cat worksheets_rna.txt); do fi # make database upload sample list header - echo "sample,worksheet,assay,referral,run,genome_build" > Gathered_Results/Database/samples_database_"$worksheet_id"_RNA.csv + echo "sample,worksheet,assay,referral,run,genome_build,coverage,ntc_coverage" > Gathered_Results/Database/samples_database_"$worksheet_id"_RNA.csv # make database upload sample list if [[ "$sample" != NTC* ]]; then