Skip to content

Headers to sample list #98

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
niamhat wants to merge 2 commits into
base: development
Choose a base branch
from
Open

Headers to sample list #98

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
975b677
adding sample database upload header for upload to svd
niamhat Aug 7, 2026
749a569
adding in coverage columns
niamhat Aug 7, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions 3_TSO500.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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,coverage,ntc_coverage" > Gathered_Results/Database/samples_database_"$worksheet_id"_RNA.csv

# make database upload sample list
if [[ "$sample" != NTC* ]]; then
Expand Down