BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-03-15T12:56:03-05:00https://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/cellranger_mkfastq/-/issues/34add checks to checkDesign process2019-11-07T12:44:19-06:00Spencer Barnesadd checks to checkDesign processAdd checks to make sure there are no spaces or extra lines in design file.Add checks to make sure there are no spaces or extra lines in design file.v2.1.5Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/9Update to bicfbase:1.12019-09-10T16:28:20-05:00Jonathan GesellUpdate to bicfbase:1.1Update to use the proper Docker images from the repo.Update to use the proper Docker images from the repo.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/8Azure Compatability2020-08-27T10:12:17-05:00Jonathan GesellAzure CompatabilityCreate the appropriate configuration scripts for running the pipeline on Azure CycleCloudCreate the appropriate configuration scripts for running the pipeline on Azure CycleCloudAzure FunctionalityJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/onboarding/-/issues/8Add in Single Cell working Group Meeting2019-09-05T11:39:51-05:00Venkat MalladiAdd in Single Cell working Group MeetingVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/37Check for space in design file error2019-11-07T16:50:49-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduCheck for space in design file errorSee cellranger_mkfastq#31See cellranger_mkfastq#31v2.1.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/33Untar folder structure2019-09-11T10:46:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUntar folder structureMcDermott sequencing core usually tar's just the folder which contains the bcl files... occasionally they include it in a bunch of sub folders.
After untaring... we need to remove those unnecessary parent folders... I would look for the...McDermott sequencing core usually tar's just the folder which contains the bcl files... occasionally they include it in a bunch of sub folders.
After untaring... we need to remove those unnecessary parent folders... I would look for the RTAComplete.txt and if not in just 1 folder... then move the containing folder to to be the root of the process... OR find a way for the process output just to output that parent dirv2.1.5Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/32Sample ID for design file2019-09-03T12:35:17-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduSample ID for design fileUser had error using example design file as template.
Example has SI-P03-C9 as the ID but current versions of the sample barcodes have the prefix SI-GA-
* [x] Replace ID in example with a SI-GA- code
* [x] In readme.md and astrocyte....User had error using example design file as template.
Example has SI-P03-C9 as the ID but current versions of the sample barcodes have the prefix SI-GA-
* [x] Replace ID in example with a SI-GA- code
* [x] In readme.md and astrocyte.yaml please add a link for the current ID's and their barcodes ```https://s3-us-west-2.amazonaws.com/10x.files/supp/cell-exp/chromium-shared-sample-indexes-plate.csv``` but you don't need to bring huge attention to it
* [x] In readme.md and astrocyte.yaml please comment on the fact that the last 2 characters is the well position of the 96-well plate that the sample barcode kit is sold in (A1 to H12)v2.1.5Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/31Design file - filename with spaces error2019-09-03T12:49:20-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduDesign file - filename with spaces errorDesign file filename with spaces throws error in checkDesign process
Preference of fixes:
1. Make spaces not matter
2. Rename file without spaces
3. Give descriptive error describing
*CHECK cellranger_count for similar error*Design file filename with spaces throws error in checkDesign process
Preference of fixes:
1. Make spaces not matter
2. Rename file without spaces
3. Give descriptive error describing
*CHECK cellranger_count for similar error*v2.1.5Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/18Add Error ignore Stratagy2019-08-28T09:32:48-05:00Jeremy MathewsAdd Error ignore StratagyError Strategy was removed when testing. Add back into pipeline.Error Strategy was removed when testing. Add back into pipeline.Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/7correct check design2019-08-28T10:47:28-05:00Jonathan Gesellcorrect check designCheck Design neededCheck Design neededJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/17Statanal Fail on single replicate2021-04-13T12:31:12-05:00Jeremy MathewsStatanal Fail on single replicateSkip statanal if # of samples is less than 2Skip statanal if # of samples is less than 2Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/30Add multiqc output to CI artifacts2019-08-14T23:31:42-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd multiqc output to CI artifactsv1.3.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/36MultiQC error2019-08-13T21:25:58-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMultiQC errorcellranger count outputs thousands with a comma surrounded by quotes:
[metrics_summary.csv](/uploads/bf7663f603940a9dbfb96b3160d4771f/metrics_summary.csv)
The count processes convert the csv to tsv:
```
sed -E 's/("([^"]*)")?,/\\2\t/g' ...cellranger count outputs thousands with a comma surrounded by quotes:
[metrics_summary.csv](/uploads/bf7663f603940a9dbfb96b3160d4771f/metrics_summary.csv)
The count processes convert the csv to tsv:
```
sed -E 's/("([^"]*)")?,/\\2\t/g' ${sample}/outs/metrics_summary.csv | tr -d "," | sed "s/^/${sample}\t/" > ${sample}_metrics_summary.tsv
```
The sed is splitting the comma in the last comma:
[BPH389PrGF_metrics_summary.tsv](/uploads/20184c06a382db3e20af3ce0af99b2cb/BPH389PrGF_metrics_summary.tsv)
That makes multiqc have throws an error because it's seeing an extra column
[.command.log](/uploads/c21552c1ce8661c4437aed92b15e9641/.command.log)
[multiqc_report.html](/uploads/3e8f11ff09e7b37e13d46656b416608f/multiqc_report.html)v1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/29Fix CountDesign2019-08-05T11:16:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix CountDesign1 bcl.tar.gz
multiple samples
= only last sample lists fastq's and it is the first sample's fastq's
see file attached:
[Cellranger_Count_Design.csv](/uploads/a4091f3f71e24fc25068c99a19181d2c/Cellranger_Count_Design.csv)1 bcl.tar.gz
multiple samples
= only last sample lists fastq's and it is the first sample's fastq's
see file attached:
[Cellranger_Count_Design.csv](/uploads/a4091f3f71e24fc25068c99a19181d2c/Cellranger_Count_Design.csv)v1.3.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/33Exclude 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/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/Astrocyte/cellranger_mkfastq/-/issues/27Add more artifacts to CI2019-07-31T12:31:14-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd more artifacts to CI* multiqc_report.html* multiqc_report.htmlv1.3.0Jeremy MathewsJeremy Mathews