Commit 49f1f62c authored by Gervaise Henry's avatar Gervaise Henry 🤠

Prep 3.0.0_indev

parent 80ae9913
Pipeline #8279 passed with stages
in 12 minutes and 24 seconds
# v3.0.0
**UserFacing**
*
**Background**
*
*Known Bugs*
* cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)
* note: 10x doesn't check github issues, emailed instead
* note: pipeline checks for spaces and exits prematurely if found
* If multiple flowcells (tar'd) files are inputted then there will be multiple fastq's by the same name, currently dealing with that name conflict is not tractable
* note: if multiple bcl files are detected then cellranger_count design file is not created
* If too many (or too large) .tar(.gz) bcl files are placed in one run, aws runs appears to fail possibly due to timeout on staging
# v2.2.0
**UserFacing**
* Update cellranger to version 4.0.0
......
......@@ -32,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.2.0"
pipelineVersion = "3.0.0_indev"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
......
......@@ -48,6 +48,6 @@ manifest {
homePage = 'https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq'
description = 'This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics (which uses Illuminas bcl2fastq). It takes bcls and demultiplexes samples from 10x Genomics Single Cell Gene Expression libraries into fastqs.'
mainScript = 'main.nf'
version = '2.2.0'
version = '3.0.0_indev'
nextflowVersion = '>=0.31.0'
}
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