BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-02-12T00:49:35-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/72Update multiqc with new singularity images2020-02-12T00:49:35-06:00Venkat MalladiUpdate multiqc with new singularity imageshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/19Update Astrocyte instructions2020-01-07T11:33:51-06:00Venkat MalladiUpdate Astrocyte instructions`One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group``One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group`Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/26Generate MultiQC report2020-02-25T07:45:39-06:00Holly RuessGenerate MultiQC reportVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/25Fix BioHPC config2020-01-07T09:38:50-06:00Holly RuessFix BioHPC configWARN: The config file defines settings for an unknown process: tssEnrich
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$checkDesignFile = <value>` with a process selector
[warm up] executor > loc...WARN: The config file defines settings for an unknown process: tssEnrich
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$checkDesignFile = <value>` with a process selector
[warm up] executor > local
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trimReads = <value>` with a process selector
[warm up] executor > slurm
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$alignReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$filterReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$experimentQC = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$convertReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$crossReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$defineExpDesignFiles = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$poolAndPsuedoReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$callPeaksMACS = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$consensusPeaks = <value>` with a process selector
Also remove GRCh37Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/14Docker Documentaion2021-04-06T08:26:21-05:00Venkat MalladiDocker DocumentaionJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/13Update Hourly Help Desk for Subtask2020-02-26T16:14:33-06:00Venkat MalladiUpdate Hourly Help Desk for SubtaskHolly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/24fix consensus peaks2020-01-07T09:35:33-06:00Holly Ruessfix consensus peaksVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/23Fix call peaks MACs2020-01-07T09:36:31-06:00Holly RuessFix call peaks MACsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/71hg37 annotate peaks fails2020-03-20T23:12:11-05:00Holly Ruesshg37 annotate peaks failsNeed to fix or remove hg37
Annotate peaks fails with this genomeNeed to fix or remove hg37
Annotate peaks fails with this genome1.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/22Make hg19 test2020-01-06T14:03:38-06:00Holly RuessMake hg19 testVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/12TOC - Fee Structure2019-12-24T22:34:44-06:00Venkat MalladiTOC - Fee StructureVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/39AWSify2020-02-21T13:10:52-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAWSifyv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/36AWSify2020-01-01T11:10:17-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAWSifyv2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/21Fix concurrent runners2020-05-28T13:59:21-05:00Venkat MalladiFix concurrent runnersVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/20Fix Pool and Pseudoreps2020-01-03T08:47:15-06:00Holly RuessFix Pool and PseudorepsVersion 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/19Fix cross correlation2020-01-03T08:47:05-06:00Holly RuessFix cross correlationVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/18Fix Convert Reads2019-12-27T14:34:30-06:00Holly RuessFix Convert ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/17Fix Experiment QC2019-12-20T10:28:15-06:00Holly RuessFix Experiment QCVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/16Fix Align Reads2019-12-16T17:14:34-06:00Holly RuessFix Align ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/15Fix Filter Reads2019-12-18T08:03:54-06:00Holly RuessFix Filter ReadsVersion 2.0Holly RuessHolly Ruess