petrov-lab/HAFpipe-line

Wrong file naming for `simpute` method

lczech opened this issue · 1 comments

lczech commented

Hi there!

There is a mismatch between the file names of the imputed table when using Task 2 with "simpute", and what Task 3 then expects as input.

In particular, see here for the command that calls Task 2, to create a table with the suffix .simpute. However, Task 2 actually names this file using the suffix .imputed instead, see here. Then, when Task 3 is called, see here, it does not find the table, as it is looking for the file with suffix .simpute instead. HAFpipe needs to be restarted with --impmethod imputed instead of simpute to fix this at the moment, which does not seem ideal.

Cheers
Lucas

greensii commented

Thank you for catching this! My apologies, i was not getting any notifications about issues/pull requests, so i am just seeing this now. But i am reviewing your pull request and really appreciate your improvements.

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