Re: Something for MoM, outreachy? TODO for workflows Fwd: bcbio_1.1.3-1_amd64.changes ACCEPTED into unstable
On Thu, 2019-03-21 at 21:52 +0100, Andreas Tille wrote:
> ChildIOException:
> File/directory is a child to another output:
> /home/andreas/debian-maintain/salsa/med-
> team/0_prospective/kallisto/test/kallisto_out
> /home/andreas/debian-maintain/salsa/med-
> team/0_prospective/kallisto/test/kallisto_out/abundance.h5
>
>
> I admit I never used snakemake and may be I'm doing something wrong.
> But its not very good in telling the user what's wrong here. Any
> hint?
I guess we are talking about
https://salsa.debian.org/med-team/kallisto/blob/master/test/Snakefile
Try deleting the output "kallisto_out" in case it masks
"kallisto_out/abundance.h5"
or it might work simply marking it as directory("kallisto_out") as in
https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#directories-as-outputs
You can then also try to change the overall output (aka all/input
reqirements) to direcxtory("kallisto_out")
--
Stian Soiland-Reyes
The University of Manchester
https://www.esciencelab.org.uk/
https://orcid.org/0000-0001-9842-9718
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