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scripts:alignment [2025/04/09 11:52] – 37.26.174.181scripts:alignment [2026/05/03 18:41] (current) – external edit 127.0.0.1
Line 67: Line 67:
 for fastq_1 in "$input_dir"/*_1.{fastq,fq}.gz; do for fastq_1 in "$input_dir"/*_1.{fastq,fq}.gz; do
     if [[ -f "$fastq_1" ]]; then     if [[ -f "$fastq_1" ]]; then
-        fastq_2="${fastq_1/_1/_2}"+        fastq_2="${fastq_1/_1․/_2․}"
         if [[ -f "$fastq_2" ]]; then         if [[ -f "$fastq_2" ]]; then
             align "$fastq_1" "$fastq_2" "$output_dir" "$reference" "$threads"             align "$fastq_1" "$fastq_2" "$output_dir" "$reference" "$threads"
Line 83: Line 83:
 #SBATCH --mem=40gb #SBATCH --mem=40gb
 #SBATCH --cpus-per-task=8 #SBATCH --cpus-per-task=8
-#SBATCH --output=../log/align_00.%j.log  # %j will be replaced with the job ID+#SBATCH --output=../log/align_00.log  
 #SBATCH --job-name=align_mydata #SBATCH --job-name=align_mydata