BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-04-08T09:17:45-05:00https://git.biohpc.swmed.edu/BICF/onboarding/-/issues/18Software Development2020-04-08T09:17:45-05:00Venkat MalladiSoftware DevelopmentVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/37Fix runners and sigbus error2020-05-08T10:01:55-05:00Venkat MalladiFix runners and sigbus errorVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/82Disk quota exceeded2020-04-13T13:50:12-05:00Venkat MalladiDisk quota exceededVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/17CI and Nextflow configuration2020-04-13T15:31:27-05:00Venkat MalladiCI and Nextflow configurationVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/81Config Lock git2020-04-16T22:21:45-05:00Venkat MalladiConfig Lock gitcan't initiate new run due to config lock
error: failed to write new configuration file /project/BICF/shared/astrocyte_test_ci/011b97be/chipseq_analysis/6415/1/80885/.tmp/git-template/config.lock
Could be some disquota issuecan't initiate new run due to config lock
error: failed to write new configuration file /project/BICF/shared/astrocyte_test_ci/011b97be/chipseq_analysis/6415/1/80885/.tmp/git-template/config.lock
Could be some disquota issueVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/80Gitlab CI overridding concurrent pipelines2020-04-16T03:01:51-05:00Venkat MalladiGitlab CI overridding concurrent pipelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/79Fix sigbus error2020-04-16T03:01:51-05:00Venkat MalladiFix sigbus errorFixing sigbus error for nextflowFixing sigbus error for nextflowVenkat MalladiVenkat Malladihttps://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/chipseq_analysis/-/issues/78Paired-end Diffbind peaks gives different answer2020-04-20T09:01:39-05:00Venkat MalladiPaired-end Diffbind peaks gives different answerJob [#79740](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/jobs/79740) failed for e09a8b62fdf02774214dee75f6096b94c7b5f8fe:Job [#79740](https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/jobs/79740) failed for e09a8b62fdf02774214dee75f6096b94c7b5f8fe:1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/16Authorship guidelines2020-03-31T12:02:51-05:00Venkat MalladiAuthorship guidelinesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/39Add base mask2020-06-20T20:34:36-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd base mask`-use-bases-mask=Y28n*,I8n*,n*,Y*``-use-bases-mask=Y28n*,I8n*,n*,Y*`v2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/77Update to Astrocyte 0.2.02020-03-21T11:16:24-05:00Venkat MalladiUpdate to Astrocyte 0.2.0astrocyte/0.2.0astrocyte/0.2.01.1.0Venkat MalladiVenkat Malladihttps://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/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/chipseq_analysis/-/issues/75Rename Plot profile to be consistent with naming2020-04-21T08:52:40-05:00Venkat MalladiRename Plot profile to be consistent with naming1.1.0Venkat MalladiVenkat Malladihttps://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/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/atacseq_analysis/-/issues/32Annotate peaks2020-06-11T16:18:58-05:00Holly RuessAnnotate peaksVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/31Blacklist of regions2020-06-09T14:55:50-05:00Holly RuessBlacklist of regionsAdd a blacklist of regions to ignore for each genomeAdd a blacklist of regions to ignore for each genomeVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/30TSS enrichment score2020-05-28T20:56:04-05:00Holly RuessTSS enrichment scoreSee ATAqc for code in python for this.See ATAqc for code in python for this.Version 2.0Holly RuessHolly Ruess