make.file with inputdir printing inputdir

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?

Thanks for the suggestion! Yes, we can add a parameter for this. You can watch the progress of the enhancement here,