galaxytools: can we somehow capture and show trimgalore's errors?
original shared history https://usegalaxy.org/u/bradlanghorst/h/custom-adapter-trimming
there was an error fetching fastqs and the inputs contained only HTML so trim galore failed, however it provided this useless message:
Trim Galore! on data 2 and data 1: trimmed reads pair 2
An error occurred with this dataset:
1.8
Cutadapt terminated with exit signal: '256'.
Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...
About this issue
- Original URL
- State: open
- Created 8 years ago
- Reactions: 1
- Comments: 15 (14 by maintainers)
Commits related to this issue
- shows warnings to give a user a fighting chance re #331 — committed to bwlang/galaxytools by bwlang 8 years ago
- shows warnings to give a user a fighting chance re #331 — committed to bwlang/galaxytools by bwlang 8 years ago
I think this is ready to go now - tests pass.