cellranger_mkfastq issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues2020-11-20T09:57:13-06:00https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/45Upgrade to cellranger 5.0.02020-11-20T09:57:13-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpgrade to cellranger 5.0.03.0.0Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/44Add ability to handle dual index2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to handle dual indexPendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/43Add output comments for untarBCL2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd output comments for untarBCLuntarBCL.sh takes FOREVER\
there are 2x `tar -t` before the actual untar\
those `tar -t` take a long time with no stdout updates
need to add echo's for stdout updatesuntarBCL.sh takes FOREVER\
there are 2x `tar -t` before the actual untar\
those `tar -t` take a long time with no stdout updates
need to add echo's for stdout updatesPendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/42Update to Astocyte 0.4.02020-09-07T06:43:20-05:00Venkat MalladiUpdate to Astocyte 0.4.0# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s18170...# Summary
New Astrocyte 0.4.0 features to test
* [x] Customized configuration file in yaml
* [x] Load specific singularity version
* [x] Load Nextflow version
* [x] Add citation in yaml file
/cc @ghenry @venkat.malladi @s181706 @s189701Venkat MalladiVenkat Malladihttps://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/40Update multiqc version/references report2020-11-03T12:04:45-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Pendinghttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/19Move params out of main.nf2019-04-26T15:47:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.edu