sra_pipeline issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues2021-07-19T13:42:12-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/30non-biological reads needs renaming2021-07-19T13:42:12-05:00Venkat Malladinon-biological reads needs renamingRejected reads are downloaded but not named appropriatley.Rejected reads are downloaded but not named appropriatley.https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/29Paired-end2021-07-19T13:41:28-05:00Venkat MalladiPaired-endPaired-end is not used anywere in the pipelinesPaired-end is not used anywere in the pipelineshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/26Fix issue downloading and spliting for single cell data2020-08-21T14:20:59-05:00Venkat MalladiFix issue downloading and spliting for single cell dataThere is an issue of properly splitting single-cell data if I, R1, R2 reads are all uploadedThere is an issue of properly splitting single-cell data if I, R1, R2 reads are all uploadedhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/19Add concatination flag2020-04-30T16:16:25-05:00Jonathan GesellAdd concatination flagAdd a flag to concatenate the resulting fastq files if there are multiple files found (default is to concat).Add a flag to concatenate the resulting fastq files if there are multiple files found (default is to concat).Astrocyte FunctionalityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/15Convert SOLID sequencing to basecall2020-06-01T13:28:23-05:00Venkat MalladiConvert SOLID sequencing to basecallSolid seqencing comes back as csqual and csfasta by default.
Use the -B option to convert to base call output to run in our pipelinesSolid seqencing comes back as csqual and csfasta by default.
Use the -B option to convert to base call output to run in our pipelinesJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/13nullDataError2020-04-20T10:55:45-05:00Jonathan GesellnullDataErrorNeeds to throw an error when srapath returns null, example:
SRS070511Needs to throw an error when srapath returns null, example:
SRS070511Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/7correct check design2019-08-28T10:47:28-05:00Jonathan Gesellcorrect check designCheck Design neededCheck Design neededJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/5Correct config2019-07-05T10:01:11-05:00Jonathan GesellCorrect configCorrecting the config files for Astrocyte and general deploymentCorrecting the config files for Astrocyte and general deploymentJonathan GesellJonathan Gesell