...
A good shell script should also be relatively easy to call. That's why, for example, we have this script takes only a short name of the desired reference and uses it to select the correct path, and only requires the name of the R1 fastq for paired-end reads, using that path to determine the name of the R2 fastq file. While we won't go into the details of that defaulting in this discussion, you might want to look at those parts of the code for ideas on how to accomplish similar goals.
The real work!
After the first part of align_bwa.sh has performed some initial error checks and established the execution environment, the script gets about doing the real work. For example, when doing a single-end alignment, it makes a call to bwa aln passing the pathname prefix for the indexed reference genome files and the input fastq file name, and redirecting the output (which normally goes to standard output) to a .sai file named using the output prefix specified by the user:
| Code Block |
|---|
bwa aln $REF_PFX $IN_FQ > $OUT_PFX.sai
ckRes $? "bwa aln";
ckFileSz "$OUT_PFX.sai";
|