Somewhere between 1.38 and 1.40 the behavior of make.file when using inputdir changed. in 1.38 the resulting file would be
sample1 inputdir/sample1_R1.fastq.gz inputdir/sample1_R2.fastq.gz
in 1.40 it’s
sample1 sample1_R1.fastq.gz sample1_R2.fastq.gz
Is there a flag that I’m missing that will control that behavior? If not, could there be one?