Do you expect rules.merge_fastqs.output to be a directory or a list of fastq files?

If I understand your post correctly, rules.merge_fastqs.output is a list of fastq files and this is passed to cellranger as a space-separated list, i.e.:

--fastqs=merged/fastq1.fastq.gz merged/fastq2.fastq.gz merged/fastq3.fastq.gz etc

However, callranger doesn't seem to support this way of passing multiple fastq files.

So I think the issue is not so much with snakemake but with the way you execute cellranger. Try running snakemake with -p option to see what commands are actually executed and check if this is what you expect.

If this doesn't help, post the rule merge_fastqs