Module 7 — Exercises

These exercises follow the lessons in order. Each one builds on the previous. Work through them in sequence, and try to write each script from memory before looking at the lessons for reference.

---

Exercise 1 — Your First Script

Write a script called hello.sh that:

1. Contains a correct shebang line
2. Prints your name
3. Prints the current date using the date command
4. Prints the message: Ready to do bioinformatics.

Make it executable and run it.

Expected output (your name and date will differ):

Alex
Wed 23 Apr 2026 10:00:00
Ready to do bioinformatics.

---

Exercise 2 — Variables and basename

Write a script called show_sample.sh that:

1. Stores the path Training/short_reads/paired/SRR1553607_2.fastq in a variable called INPUT
2. Uses basename and $() to extract just the sample name — without the directory path or the .fastq extension — and stores it in a variable called SAMPLE
3. Prints both the full path and the clean sample name

Expected output:

Full path: Training/short_reads/paired/SRR1553607_2.fastq
Sample name: SRR1553607_2

---

Exercise 3 — A Simple Loop

Write a script called list_samples.sh that:

1. Loops over every .fastq file in Training/short_reads/paired/
2. For each file, prints a line in this format:

Found sample: SRR1553607_1
Found sample: SRR1553607_2

Use basename inside the loop to get the clean sample name.

---

Exercise 4 — Log Files

Write a script called log_samples.sh that:

1. Stores the log filename sample_list.txt in a variable called LOG
2. Uses > to write the line Sample list into the log file at the start
3. Loops over every .fastq file in Training/short_reads/paired/
4. For each file, uses >> to append the clean sample name to the log
5. Prints Log saved to: sample_list.txt to the terminal when finished

After running the script, check the contents of sample_list.txt. It should contain:

Sample list
SRR1553607_1
SRR1553607_2

---

Exercise 5 — Capturing All Output with exec

Write a script called exec_log.sh that:

1. Defines a variable LOG_FILE="full_run.log"
2. Uses exec > >(tee $LOG_FILE) 2>&1 to capture everything — stdout and stderr — to the terminal and the log file simultaneously
3. Prints Run started
4. Loops over every .fastq file in Training/short_reads/paired/, printing Processing: [sample_name] for each one
5. Prints Run finished

After running the script:

• Confirm the messages appeared in the terminal
• Confirm full_run.log contains the same messages

Then try this variation: change the exec line to exec 2> errors.log and run it again. Notice that normal output still prints to the terminal — only errors would be captured in errors.log.

---

Exercise 6 — Build Your Own Pipeline Script

Write a script called my_qc_pipeline.sh that:

1. Defines DATA_DIR, OUTPUT_DIR, and LOG_FILE as variables at the top
2. Uses exec > >(tee $LOG_FILE) 2>&1 so all output is captured automatically
3. Creates the output directory using mkdir -p
4. Loops over every .fastq file in DATA_DIR
5. For each file:
   • Prints Quality checking: [sample_name]
   • Runs fastqc $FILE --outdir $OUTPUT_DIR
6. Prints Pipeline complete. when the loop finishes

Write this script from scratch. Use Lesson 6 as a reference only if you are stuck.