MAKE_GENE_BED making 0kb .bed files

[hcliedtke]

Hi, I am using this really nice pipeline on my dataset. I am using an in-house reference genome and currently with the conda profile (I know that singularity or docker would be better, but for the time being this is the only option I have).

The pipeline fails at MERGED_LIB_PLOTPROFILE and I think I have traced it back to the fact that the .bed file supplied to the computeMatrix function is empty (0 kb).

I have looked at the report and execution report and I believe the problem is with MAKE_GENE_BED, which executes the script gtf2bed foo.gtf > foo.bed. It seems to be that this should be gtf2bed < foo.gtf > foo.bed. Could this be?

Thanks for your help. I am relatively new to nextflow pipelines, so apologies if I am not expressing my issue in the best way.