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Does the pipeline-level stub test actually work? I...
# sarek_dev
a
Does the pipeline-level stub test actually work? I am finding that the 
options
appears to be overwritten when using 
stub: true
by the second designation of 
options "-output-dir $outputDir"
.
👀 1
m
I haven't tried them in a while, they might be totally out of date
Let me try that real quick
yeah, you are totally right, let me push a fix right now
👍 1
That being said, we are lacking proper support for stub in sarek, as I feel we are missing some stubs in some modules
a
How are you running these tests locally Maxime? Because I have found that 
.nf-test
is not masked for me?
e.g. 
launchDir: [PATH]/.nf-test/tests
instead of 
[PATH]/tests
m
nf-test test .... --tag cpu_stub,cpu_conda_stub tests/
Oh you meant the local path
Yeah that's an issue
I had to put a hack to get the path right
a
But are you setting 
NFT_WORKDIR
? I looked at the code for 
nft-utils
and it specifically masks that but if you don’t set a default and it goes to 
$(pwd)/.nf-test
then it seems that 
.nf-test
is not masked?
m
But since coming Nextflow is getting output in the log, I will probably have to ditch the capture or the full capture of std out
Give me five to get to a computer
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