Hey, I am using a command line tool (bwa mem). it's not so important what it does, but that it somehow changed it's behavior in macOS zsh. A command that worked earlier does now not work anymore. The intended usage of this tool is:
Usage: bwa mem [options] <idxbase> <in1.fq> [in2.fq]
Some time ago (about 1 year) I wrote a workflow that contained this command:
bwa mem resources/genome.fasta path/to/read_1.fastq.gz path/to/read_2.fastq.gz -K 100000000 -Y
So, I put the options behind the positional arguments, not in front of it. It's not its intended usage, I know, but it always worked. I retried that yesterday and all of a sudden, zsh complains about incorrect usage and I have to change the order of the arguments.
I don't use a newer version of bwa (fixed by conda install). The old command still works on centOS bash. I installed bwa 0.7.17 freshly on both OSs and centOS bash runs the command without complaining, whereas macOS zsh does not. Has there been any change in zsh that would explain this?