Luka Stojanovic
Luka Stojanovic
Then it wouldn't be much different than just unpacking tarball :)
This is what the spec has to say about booleans: > boolean: If true, add prefix to the command line. If false, add nothing. Unfortunately, I can't find if it's...
It's implemented on a tool level in the cottontail editor, where you can preview generated command with provided inputs, but I guess could also be added to bunny relatively easily....
I've tried to run GDC (transform.cwl) workflow with code from [feature/gdc](https://github.com/rabix/bunny/tree/feature/gdc) branch, but got the following error: zcat SRR622461_2.fq.gz | /usr/local/bin/fastq_remove_duplicate_qname - | gzip - > SRR622461_2.fq.gz: not found Good...
It's a bunny branch with some gdc related fixes.
@jeremiahsavage I tried running it that way too, but failed with same error. Will continue debugging...
Yup. I was having for some reason a gdc pipeline directory without `.git`. And it was in another dir, that was a git repo, so when I did git pull,...
One minor issue we had to fix: NCI-GDC/gdc-dnaseq-cwl#51
@jeremiahsavage bunny doesn't do anything to prevent network connectivity from container. Let's take a step back and figure out what the actual problem is. I would dare to guess that...
@jeremiahsavage I'm still confused about what is about your networking situation that demands host network? What are you trying to fetch that can't be accessed through a bridge network? Which...