BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-03-15T12:55:45-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/76Update version of multiqc2020-03-15T12:55:45-05:00Holly RuessUpdate version of multiqcuse image /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.imguse image /project/shared/bicf_workflow_ref/singularity_images/bicf-multiqc-2.0.0.img1.1.0Venkat MalladiVenkat Malladihttps://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/26Generate MultiQC report2020-02-25T07:45:39-06:00Holly RuessGenerate MultiQC reportVersion 2.0Holly RuessHolly Ruesshttps://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/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/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/KCE/kce_etl/-/issues/9Surgery Table2020-01-28T13:59:24-06:00Venkat MalladiSurgery Tablehttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/15Make a link in redmine.md2020-01-24T11:00:54-06:00Venkat MalladiMake a link in redmine.mdVenkat MalladiVenkat Malladihttps://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/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/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/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/22Make hg19 test2020-01-06T14:03:38-06:00Holly RuessMake hg19 testVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/7Shift is incorrect for ATAC-seq2020-01-06T13:57:44-06:00Venkat MalladiShift is incorrect for ATAC-seqShift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Shift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Version 2.0Holly RuessHolly Ruesshttps://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/2deeptools version 3 error2020-01-02T14:27:29-06:00Spencer Barnesdeeptools version 3 errorWhen calculating signal using bamCoverage, deeptools version 3 does not recognize output of filter_reads step as bam files. Deeptools version 2.5.* does work currently.When calculating signal using bamCoverage, deeptools version 3 does not recognize output of filter_reads step as bam files. Deeptools version 2.5.* does work currently.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/3mitochondrial chromosome reads2020-01-02T14:26:27-06:00Spencer Barnesmitochondrial chromosome readsRe-write script to remove mitochondrial reads as an option. We should also get the percentage of mitochondrial reads in all reads.Re-write script to remove mitochondrial reads as an option. We should also get the percentage of mitochondrial reads in all reads.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/4pool and pseudoreplicate2020-01-02T14:24:34-06:00Spencer Barnespool and pseudoreplicatepool_and_pseudoreplicate.py script creates temporary working files which interfere with one another when running various instances in the same directory.pool_and_pseudoreplicate.py script creates temporary working files which interfere with one another when running various instances in the same directory.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/5Re-direct output2020-01-02T14:24:08-06:00Holly RuessRe-direct outputAdd an option to name the output folderAdd an option to name the output folderVersion 2.0Holly RuessHolly Ruess