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Create test for ALFA

    • Closed Issue created by Dominik Burri @burri0000

    In order to ensure that ALFA runs for different configurations, we need tests. For this do the following:

    • create a test sample table (e.g. for parts of chr21.bam) with the information about the sample
    • create a test case
    • write a bash script that executes snakemake with the proper settings
    • adjust .gitlab-ci.yml with the new bash script that executes the ALFA parts
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    • Alex Kanitz
      Alex Kanitz @kanitz ·
      Owner

      This sounds great. However, as this should all be done for every rule that is going to be added to the pipeline in the future, we do not really need a separate issue for that. Apart from cluttering the issue board, it introduces the risk of pulling in even more untested (and potentially faulty) code. Note that this is different from tests for rules that are already in the pipeline. These unfortunately will need to be added retroactively, warranting individual issues.

      I have closed this issue and added the info to #18 (closed).

    • Alex Kanitz closed

      closed

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