Commit 364d3816 authored by Gervaise Henry's avatar Gervaise Henry 🤠

Add cellranger 4.0.0

parent 4a6e4222
Pipeline #7528 failed with stages
in 327 minutes and 54 seconds
# v2.2.0-indev
**UserFacing**
* Update cellranger to version 4.0.0
**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
# v2.1.5
**UserFacing**
* Check Design File for spaces in name and file contents
......
......@@ -32,7 +32,7 @@ bclCount = Channel
.count()
// Define regular variables
pipelineVersion = "2.1.5"
pipelineVersion = "2.2.0-indev"
name = params.name
designLocation = Channel
.fromPath(params.designFile)
......@@ -152,7 +152,7 @@ process mkfastq {
tag "${bcl.simpleName}"
publishDir "${outDir}/${task.process}", mode: 'copy', pattern: "{*/outs/**/*.fastq.gz}"
queue '128GB,256GB,256GBv1,384GB'
module 'cellranger/3.1.0:bcl2fastq/2.19.1'
module 'cellranger/4.0.0:bcl2fastq/2.19.1'
input:
file versions_cellrangerScript
......
......@@ -47,6 +47,6 @@ 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 = '2.1.5'
version = '2.2.0-indev'
nextflowVersion = '>=0.31.0'
}
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