BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-09-03T12:49:20-05:00https://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/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/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/atacseq_analysis/-/issues/32Annotate peaks2020-06-11T16:18:58-05:00Holly RuessAnnotate peaksVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/33New folders for all steps2019-03-16T19:26:26-05:00Venkat MalladiNew folders for all stepsBreak steps into sub-folders by Sample, or Experiment where appropriateBreak steps into sub-folders by Sample, or Experiment where appropriate1.0.0Venkat MalladiVenkat Malladihttps://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/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruesshttps://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/chipseq_analysis/-/issues/34Fix tests for software versions2019-04-20T03:12:15-05:00Venkat MalladiFix tests for software versions1.0.0Venkat 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/atacseq_analysis/-/issues/34Diff Peak analysis2020-06-23T16:02:40-05:00Holly RuessDiff Peak analysisVersion 2.1.0Holly RuessHolly Ruesshttps://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/chipseq_analysis/-/issues/35Fix astrocyte run2019-04-22T15:17:51-05:00Venkat MalladiFix astrocyte runAstrocyte is not using the correct variables in Main.nfAstrocyte is not using the correct variables in Main.nf1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/35Cleanup process outputs2019-11-08T10:30:03-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduCleanup process outputsv2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/35Change to 256 only if job fails2020-06-23T16:02:34-05:00Holly RuessChange to 256 only if job failsMay need to incorporate maxErrors and maxRetries into processesMay need to incorporate maxErrors and maxRetries into processesVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/38Add 3':5' param2020-04-14T09:53:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 3':5' paramv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/41Containerize2020-04-15T21:18:39-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduContainerizev2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/42Update params to current standards2020-04-15T10:04:24-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate params to current standardsnon-imputable params do not need to have "param." prefixnon-imputable params do not need to have "param." prefixv2.1.1Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/36Update Astrocyte documentation and errors2019-04-22T22:18:14-05:00Venkat MalladiUpdate Astrocyte documentation and errors1.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/36AWSify2020-01-01T11:10:17-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAWSifyv2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu