Bash Scripting for Bioinformatics
Script Template
#!/bin/bash
set -euo pipefail
# Configuration
THREADS=8
INPUT_DIR="${1:?Usage: $0 <input_dir> <output_dir>}"
OUTPUT_DIR="${2:?Usage: $0 <input_dir> <output_dir>}"
log() { echo "[$(date '+%H:%M:%S')] $1" >&2; }
mkdir -p "$OUTPUT_DIR"
log "Starting..."
Variables
sample="BRCA_001"
threads=8
out="${results_dir}/${sample}.bam" # ${} safer when appending
current_date=$(date +%Y-%m-%d) # command substitution
n
[Description truncada. Veja o README completo no GitHub.]
