BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-07-31T23:55:49-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/28Exclude changes in *.md for CI2019-07-31T23:55:49-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduExclude changes in *.md for CIexcept:
changes:
- "*.md"except:
changes:
- "*.md"Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/7Add Addtional ORCID2019-08-02T10:08:40-05:00Venkat MalladiAdd Addtional ORCIDhttps://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/KCE/kce_etl/-/issues/15Image table2019-11-23T14:56:17-06:00Venkat MalladiImage tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/14Followup table2020-04-22T16:54:18-05:00Venkat MalladiFollowup tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/11Metastasis table2020-04-25T18:53:48-05:00Venkat MalladiMetastasis tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/9Surgery Table2020-01-28T13:59:24-06:00Venkat MalladiSurgery Tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/8Biopsy2021-08-12T13:52:31-05:00Venkat MalladiBiopsyhttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/6Cancer Gene Table2019-10-24T10:55:23-05:00Venkat MalladiCancer Gene Tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/5Supportive Meds table2019-12-12T08:35:26-06:00Venkat MalladiSupportive Meds tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/4Cancer Drug Table2019-12-12T08:35:41-06:00Venkat MalladiCancer Drug Tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/3Labs table2019-09-25T14:32:40-05:00Venkat MalladiLabs tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/2Vital table2019-09-25T14:48:39-05:00Venkat MalladiVital tablehttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/1Radiation Table2019-12-12T08:31:20-06:00Venkat MalladiRadiation Tablehttps://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 Mathews2019-07-03https://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/6Docker Image Integration2019-07-18T16:18:45-05:00Jonathan GesellDocker Image IntegrationTest for integrating Docker imagesTest for integrating Docker imagesJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/5Correct config2019-07-05T10:01:11-05:00Jonathan GesellCorrect configCorrecting the config files for Astrocyte and general deploymentCorrecting the config files for Astrocyte and general deploymentJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/6ADD TO2019-11-15T10:34:11-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduADD TOHolly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/16CheckDesignFile process2019-07-08T21:20:43-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCheckDesignFile processnextflow.config sets all process to run on '128GB,256GB,256GBv1' nodes
```
process.queue='128GB,256GB,256GBv1'
```
that means that even the checkdesignfile process needs to wait on a high power process
you can make checkdesignfile bypas...nextflow.config sets all process to run on '128GB,256GB,256GBv1' nodes
```
process.queue='128GB,256GB,256GBv1'
```
that means that even the checkdesignfile process needs to wait on a high power process
you can make checkdesignfile bypass that to run on a super by:
```
process checkdesignfile {
queue 'super'
...
```Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/variant_germline/-/issues/2Fix SubModules2019-06-11T11:10:15-05:00Jeremy MathewsFix SubModulespossible solution: https://docs.gitlab.com/ee/ci/git_submodules.htmlpossible solution: https://docs.gitlab.com/ee/ci/git_submodules.htmlJeremy MathewsJeremy Mathews