chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2021-08-05T10:22:15-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/92Insert vizapp code2021-08-05T10:22:15-05:00Erand SmakajInsert vizapp codeThe R Scripts for vizapp (server.R and ui.R) seem to contain incorrect code (it contains the HTML for gitlab login page instead of R scripts)
Please substitute with the correct vizapp code.
https://git.biohpc.swmed.edu/BICF/Astrocyte/c...The R Scripts for vizapp (server.R and ui.R) seem to contain incorrect code (it contains the HTML for gitlab login page instead of R scripts)
Please substitute with the correct vizapp code.
https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/tree/dev/vizapphttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/91Update nf-tower token2021-07-25T17:02:51-05:00Venkat MalladiUpdate nf-tower token2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/90Strip spaces in design file2020-12-29T17:26:45-06:00Venkat MalladiStrip spaces in design fileStrip leading or trailing spaces in design fileStrip leading or trailing spaces in design file2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/89Diffbind is tsv not csv2020-12-29T17:23:49-06:00Venkat MalladiDiffbind is tsv not csvDiffbind output is actually tsv not csv file forat.Diffbind output is actually tsv not csv file forat.2.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/88create down-sampled test data2020-08-07T10:17:20-05:00Spencer Barnescreate down-sampled test dataCreate down-sampled fastq's for quick tests when applying bug fixes.Create down-sampled fastq's for quick tests when applying bug fixes.Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/87Annotation file is missing data2020-08-07T21:10:52-05:00Venkat MalladiAnnotation file is missing dataSymbol is missing in annotation file
Headers are off by oneSymbol is missing in annotation file
Headers are off by one2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/86Update to astrocyte 0.3.12020-07-01T14:35:06-05:00Venkat MalladiUpdate to astrocyte 0.3.12.0.0Venkat MalladiVenkat Malladihttps://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/84Track chip-seq usage2020-07-01T14:32:45-05:00Venkat MalladiTrack chip-seq usage```
/*
* trackStart: track start of pipeline
*/
process trackStart {
script:
"""
hostname
ulimit -a
export https_proxy=\${http_proxy}
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow....```
/*
* trackStart: track start of pipeline
*/
process trackStart {
script:
"""
hostname
ulimit -a
export https_proxy=\${http_proxy}
curl -H 'Content-Type: application/json' -X PUT -d '{ \
"sessionId": "${workflow.sessionId}", \
"pipeline": "atacseq_analysis", \
"start": "${workflow.start}", \
"astrocyte": ${params.astrocyte}, \
"status": "started", \
"nextflowVersion": "${workflow.nextflow.version}", \
"pipelineVersion": "2.0.0", \
"ci": ${params.ci}, \
"dev": ${params.dev}}' \
"https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
"""
}
```Venkat MalladiVenkat Malladihttps://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/82Disk quota exceeded2020-04-13T13:50:12-05:00Venkat MalladiDisk quota exceededVenkat 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/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/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/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/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/73Single Rep Pool and Pseudo2020-03-24T11:46:18-05:00Venkat MalladiSingle Rep Pool and PseudoCheck if for a single rep pool and pseudo replicate works based on new refactored code.Check if for a single rep pool and pseudo replicate works based on new refactored code.1.1.1Venkat MalladiVenkat Malladi