Hi Stian, On Fri, Mar 22, 2019 at 09:18:22AM +0000, Stian Soiland-Reyes wrote: > 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
That's correct. > Try deleting the output "kallisto_out" in case it masks > "kallisto_out/abundance.h5" There is no such directory inside upstream tarball and thus not inside the packaging directory since it was imported into the packaging repository. > 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 I understand your hint as suggesting the following diff: diff --git a/test/Snakefile b/test/Snakefile index 1b2759c..382f763 100644 --- a/test/Snakefile +++ b/test/Snakefile @@ -6,6 +6,8 @@ INDEX = "{0}.kidx".format(PRE) rule all: input: "kallisto_out/abundance.h5" + output: + directory("kallisto_out") rule index: input: FASTA > You can then also try to change the overall output (aka all/input > reqirements) to direcxtory("kallisto_out") Unfortunately this did not change anything. Thanks for your attempt to help in any case Andreas. -- http://fam-tille.de