BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-06-16T09:35:08-05:00https://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/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/cellranger_count/-/issues/10Add ability to count additional features2020-06-21T13:57:51-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to count additional featureshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customPendingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/85Update multiqc version/references report2020-06-23T15:48:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/83Unique Experiment check2020-06-23T15:49:10-05:00Venkat MalladiUnique Experiment checkCheck design file for unique experiments and replicates before starting.Check design file for unique experiments and replicates before starting.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/74Annotepeaks2020-06-23T15:49:23-05:00Venkat MalladiAnnotepeaksSeperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.Seperate annotate peaks with different design file reading to chunk processing so it doesn't read it into memory.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/9Add in blacklist2020-06-23T15:50:34-05:00Venkat MalladiAdd in blacklistAdd blacklist support for mm9,mm10,hg19,hg38Add blacklist support for mm9,mm10,hg19,hg382.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/14Add in peak call with SPP and IDR2020-06-23T15:50:40-05:00Venkat MalladiAdd in peak call with SPP and IDR2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/39Optimizations2020-06-23T15:51:07-05:00Jonathan GesellOptimizationsGeneral speed-ups and optimization of pipeline branches.General speed-ups and optimization of pipeline branches.3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/44diffbind design file error2020-06-23T15:51:25-05:00Spencer Barnesdiffbind design file errorThe step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would cha...The step that creates the diffbind design file copies the SampleID column into the Condition column. This causes an error since this causes diffbind to compare N different conditions instead of the expected 2 or 3. Possible fix would change the diffbind script to compare Factor or Treatment as default.2.0.0Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/60Make both astrocyte compatable and other cluster compatable2020-06-23T15:51:53-05:00Holly RuessMake both astrocyte compatable and other cluster compatableWe need to move the module load from the main.nf into if astrocyte = True statement.We need to move the module load from the main.nf into if astrocyte = True statement.3.0.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/69add checks to determine if fastq files are in proper format and not truncated2020-06-23T15:52:26-05:00Spencer Barnesadd checks to determine if fastq files are in proper format and not truncatedWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidatorWe can maybe implement this tool:
https://genome.sph.umich.edu/wiki/FastQValidator2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/64Containerization2020-06-23T15:52:34-05:00Jonathan GesellContainerizationContainerize as much of the ChipSeq pipeline as possible, perferably with one container per processContainerize as much of the ChipSeq pipeline as possible, perferably with one container per process3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/32Memory2020-06-23T15:56:18-05:00Venkat MalladiMemoryChange Python max mem to maybe 3/4 (test), for samtools sortChange Python max mem to maybe 3/4 (test), for samtools sort3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/36update version of nextflow2020-06-23T16:02:27-05:00Holly Ruessupdate version of nextflowupdate nextflow/0.31.0 to nextflow/19.09.0update nextflow/0.31.0 to nextflow/19.09.0Version 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/35Change to 256 only if job fails2020-06-23T16:02:34-05:00Holly RuessChange to 256 only if job failsMay need to incorporate maxErrors and maxRetries into processesMay need to incorporate maxErrors and maxRetries into processesVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/34Diff Peak analysis2020-06-23T16:02:40-05:00Holly RuessDiff Peak analysisVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/1map_reads failure case2020-06-23T16:03:04-05:00Spencer Barnesmap_reads failure caseWhen map_reads.py fails to find the input files, empty bam files are still created. This should probably give a non zero exit status instead.When map_reads.py fails to find the input files, empty bam files are still created. This should probably give a non zero exit status instead.Version 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/25update test for astrocyte 0.3.12020-06-26T15:38:59-05:00Venkat Malladiupdate test for astrocyte 0.3.1Add test for astrocyte
update Readme to have astrocyte badgeAdd test for astrocyte
update Readme to have astrocyte badge