cellranger_mkfastq issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues2020-10-30T11:48:42-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/41Add test for astrocyte specific run of pipline2020-10-30T11:48:42-05:00Venkat MalladiAdd test for astrocyte specific run of pipline# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701# Summary
* [x] Add test for astrocyte-specific test besides cli
* [x] Add Badge for astrocyte
* [x] Test for astrocyte 0.4.0 instead of loading astrocyte
/cc @ghenry @venkat.malladi @s181706 @s189701https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/37Add ulimit to cellranger process2020-06-20T20:34:35-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ulimit to cellranger processsee: BICF/Astrocyte/cellranger_count#40see: BICF/Astrocyte/cellranger_count#40v2.1.5Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/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/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_mkfastq/-/issues/15Fix astrocyte regex2019-04-26T01:34:28-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix astrocyte regex```
regex: ".*csv"
```
to
```
regex: "*.csv"
``````
regex: ".*csv"
```
to
```
regex: "*.csv"
```v1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/13Handle multi-flowcells in fastqc and multiqc2019-04-26T01:34:06-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduHandle multi-flowcells in fastqc and multiqcv1.1.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu