stjudecloud/workflows

NGSderive step assumes plain text

adthrasher opened this issue · 1 comments

adthrasher commented

All of the other steps that use the GTF file seem to properly handle compressed input, but this step requires the file to be plain-text. It should handle compressed input appropriately.

workflows/tools/ngsderive.wdl

Line 21 in f19e0d3

sort -k1,1 -k4,4n -k5,5n ~{gtf} | bgzip > annotation.gtf.gz

a-frantz commented

This has been resolved