mkdir GA3 cd GA3 touch README.md mkdir data scripts results cp -v ../garrigos-data/fastq/ERR10802863* data/ cp -v ../garrigos-data/meta/metadata.tsv data/ git init echo "data/" > .gitignore echo "results/" >> .gitignore

git add README.md git commit -m "Finished Part A"

PART B

touch scripts/echo.sh bash scripts/echo.sh Oct07 Oct08 bash scripts/echo.sh Oct07 Oct08 Oct09 Oct10 bash scripts/echo.sh Oct07 Oct08 "Oct09 Oct10"

touch scripts/concat.sh bash scripts/concat.sh data/_R1. data/_R2. results/combined_file.fastq.gz

touch scripts/printline.sh bash scripts/printline.sh data/metadata.tsv 10 bash scripts/printline.sh data/metadata.tsv 15 > results/line_15

metadata=metadata.tsv line_number=15

bash scripts/printline.sh data/"$metadata" "$line_number" > results/"$metadata"_"$line_number"

apptainer exec oras://community.wave.seqera.io/library/trim-galore:0.6.10--bc38c9238980c80e trim_galore -v

apptainer exec oras://community.wave.seqera.io/library/trim-galore:0.5.0--16bd677ee493f6cd trim_galore -v

pandoc -v

module spider pandoc module load pandoc/3.6.4 pandoc -o README.pdf README.md

git remote add origin git@github.com:Menukabh/GA3.git git commit -m "finished" git add scripts/ git branch -M main git push -u origin main

git add README.md .gitignore