chipseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues2020-08-07T21:10:52-05:00https://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/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/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/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 Malladihttps://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/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/chipseq_analysis/-/issues/68Remove artifacts2020-03-15T12:55:54-05:00Venkat MalladiRemove artifacts1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/67Python Version not in Software Version2020-03-15T12:56:03-05:00Venkat MalladiPython Version not in Software Version![Screen_Shot_2019-09-19_at_8.16.13_AM](/uploads/d1f69416b9c4ef171560506c7bcca5d3/Screen_Shot_2019-09-19_at_8.16.13_AM.png)
Update
`
Python': ['version_python.txt', r"python, version (\S+)"],
`![Screen_Shot_2019-09-19_at_8.16.13_AM](/uploads/d1f69416b9c4ef171560506c7bcca5d3/Screen_Shot_2019-09-19_at_8.16.13_AM.png)
Update
`
Python': ['version_python.txt', r"python, version (\S+)"],
`1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/66Software References aren't in Multic2020-03-15T12:56:10-05:00Venkat MalladiSoftware References aren't in Multic1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/65Testing fails on new update2020-03-15T12:56:23-05:00Venkat MalladiTesting fails on new updateTesting fails when adding:
`pytest -m singleend`
`pytest -m pairedend`
For multiple, need to update test orderTesting fails when adding:
`pytest -m singleend`
`pytest -m pairedend`
For multiple, need to update test order1.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/61add python version to multiqc process2019-07-19T08:32:16-05:00Spencer Barnesadd python version to multiqc processCurrently, the multiqc html does not list the python version used in the pipeline. Main.nf should be modified to produce a 'version_python.txt' file and the generate_versions.py should be modified such that its output, 'software versions...Currently, the multiqc html does not list the python version used in the pipeline. Main.nf should be modified to produce a 'version_python.txt' file and the generate_versions.py should be modified such that its output, 'software versions', includes the python version.Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/59update 'reference.md'2019-07-09T08:58:33-05:00Spencer Barnesupdate 'reference.md'The Nextflow publication should be added to the reference list.
Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology...The Nextflow publication should be added to the reference list.
Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.Jeremy MathewsJeremy Mathews2019-07-03