sra_pipeline issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues2020-08-26T11:06:35-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/27Add flag for SAM instead of FastQ2020-08-26T11:06:35-05:00Jonathan GesellAdd flag for SAM instead of FastQCreate an option if users want to download the SAM file instead of the FastQ files.Create an option if users want to download the SAM file instead of the FastQ files.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/24Containerize Pipeline2020-06-17T16:37:54-05:00Jonathan GesellContainerize PipelineDesign the container so that it can be run by Docker as one image.Design the container so that it can be run by Docker as one image.Azure FunctionalityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/22Parallelize tests2020-06-16T09:35:08-05:00Jonathan GesellParallelize testsRe-write the tests using a combination of joblib.Parallel and pytest-parallel to see if we can speed up the tests. Note: on Nucleus009, we want to keep the core usage count down to no more than 4 cores.Re-write the tests using a combination of joblib.Parallel and pytest-parallel to see if we can speed up the tests. Note: on Nucleus009, we want to keep the core usage count down to no more than 4 cores.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/14updateUnitTests2020-06-17T05:53:20-05:00Jonathan GesellupdateUnitTestsThe tests need to be updated to the following style:
Unit Tests: Test the individual commands in the pipeline for logic and functionality
Integration Tests: Runs the pipeline end-to-end and verifies that it runs without issue
Consistency...The tests need to be updated to the following style:
Unit Tests: Test the individual commands in the pipeline for logic and functionality
Integration Tests: Runs the pipeline end-to-end and verifies that it runs without issue
Consistency Tests: Tests the pipeline outputs to ensure that they are consistent from version to version.Singularity 2.0.0 CompatabilityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/12Update to Singularity Image 2.0.0 compatability.2020-02-05T14:52:20-06:00Jonathan GesellUpdate to Singularity Image 2.0.0 compatability.Singularity 2.0.0 CompatabilityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/9Update to bicfbase:1.12019-09-10T16:28:20-05:00Jonathan GesellUpdate to bicfbase:1.1Update to use the proper Docker images from the repo.Update to use the proper Docker images from the repo.Jonathan GesellJonathan Gesell