style-guide.md

Style Guide

This style guide provides best practices and conventions for writing scripts hosted within this repostiroy.

1. Shebang Line

• Always start your script with the shebang line to specify the script's interpreter.

  #!/bin/bash

2. Comments

• Use comments to explain the purpose of the script, major steps, and any complex logic.

• Add a comment at the beginning of the script describing its purpose.

• Use inline comments sparingly to clarify specific lines of code.

  # Get the directory of the current script
  SCRIPT_DIR=$(dirname "$0")

3. Variables

• Use uppercase letters for variable names to distinguish them from commands and make them easily recognizable.

• Use meaningful variable names that convey their purpose.

  FASTQ_FILE=$1

4. Input Validation

• Always validate inputs to ensure the script behaves as expected.

• Provide clear and user-friendly error messages.

• Use exit 1 to terminate the script if validation fails.

  if [ "$#" -ne 1 ]; then
      echo "Usage: $0 <fastq_file>"
      exit 1
  fi
  
  if [ ! -f "$FASTQ_FILE" ]; then
      echo "Error: File '$FASTQ_FILE' not found!"
      exit 1
  fi

5. Output Messages

• Use echo to display informative messages to the user.

• Clearly indicate the progress and results of the script's operations.

  echo "Processing FASTQ file: $FASTQ_FILE"

6. Commands and Calculations

• Use $(...) for command substitution instead of backticks for better readability and nesting.

• Break down complex calculations into smaller, understandable steps with comments.

  ## Count the number of lines in the FASTQ file
  LINE_COUNT=$(wc -l < "$FASTQ_FILE")
  ## Calculate the number of reads (4 lines per read)
  READ_COUNT=$((LINE_COUNT / 4))
  
  echo "Number of reads in $FASTQ_FILE: $READ_COUNT"

7. Indentation

• Use four spaces for indentation instead of tabs to ensure consistency across different editors and environments.

  if [ "$#" -ne 1 ]; then
      echo "Usage: $0 <fastq_file>"
      exit 1
  fi

8. Exiting the Script

• Use exit 0 to explicitly indicate successful completion of the script, although it is not always necessary as Bash implicitly exits with the status of the last executed command.

Example Script with Comments

#!/bin/bash

# This script processes a FASTQ file and counts the number of reads.

# Get the directory of the current script
SCRIPT_DIR=$(dirname "$0")

# Check if a FASTQ file is provided
if [ "$#" -ne 1]; then
    echo "Usage: $0 <fastq_file>"
    exit 1
fi

FASTQ_FILE=$1

# Check if the provided file exists
if [ ! -f "$FASTQ_FILE" ]; then
    echo "Error: File '$FASTQ_FILE' not found!"
    exit 1
fi

echo "Processing FASTQ file: $FASTQ_FILE"

# Count the number of reads in FASTQ file
## Count the number of lines in the FASTQ file
LINE_COUNT=$(wc -l < "$FASTQ_FILE")
## Calculate the number of reads (4 lines per read)
READ_COUNT=$((LINE_COUNT / 4))

echo "Number of reads in $FASTQ_FILE: $READ_COUNT"

Following this style guide will help ensure your scripts are easy to read, maintain, and understand by others.