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Thank you, @evanfloden, for bringing this bug to our attention. You are correct!
We made some changes to the code last week, moving this functionality to a nextflow process rather than relying on groovy. Hopefully, this resolves the error. Please test our dev branch and inform us if the issue persists.
Description of the bug
The ped file cannot be created when outdir is an s3 path, leading to an error.
For example, defining
--outdir s3:/rarediseases-workspace/results/
with the test data gives this error:I believe it is originating from this code, although the single s3:/ is also suspicious.
Command used and terminal output
Relevant files
No response
System information
No response
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