Commit cadc1dea authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Merge branch '56-5GEX' into 'develop'

Resolve "Add 5GEXPE/SE as library options"

Closes #56

See merge request !80
parents 70e3c6e4 911127be
Pipeline #8396 passed with stages
in 15 minutes and 43 seconds
# v3.0.0
**User Facing**
*
* Add 5GEX-PE, 5GEX-R2, threeprime as library options
**Background**
*Known Bugs*
* Vizapp does not yet work for Astrocyte
* Running in CLI: to set --fastq path of file/s needs to be in quotes
* 2020-A references don't work with with cellranger versions < 4.0.0 (bug)
# v2.2.0
**User Facing**
......
......@@ -96,9 +96,12 @@ To Run:
* --version (cellranger version) 2.1.1 can only read --kitVersion of two (2)
* options:
* *'auto'*
* *'3GEX'*
* *'3GEXv3'*
* *'3GEXv2'*
* *'5GEX'*
* *'5GEXPE'*
* *'5GEXR2'*
* eg: **--kitVersion '3GEXv3'**
* **--version**
* cellranger version
......
......@@ -140,9 +140,12 @@ workflow_parameters:
default: 'auto'
choices:
- ['auto', 'Auto Detect']
- ['3GEX', '3prime GEX Auto (3prime Gene Expression)']
- ['3GEXv3', '3prime GEX v3 (3prime Gene Expression)']
- ['3GEXv2', '3prime GEX v2 (3prime Gene Expression)']
- ['5GEX', '5prime GEX Auto (5prime Gene Expression)']
- ['5GEXPE', '5prime GEX both R1 and R2 used for alignment (5prime Gene Expression)']
- ['5GEXR2', '5prime GEX only R2 used for alignment (5prime Gene Expression)']
required: true
description: |
10x single cell gene expression chemistry version (only used in cellranger version 3.x).
......
......@@ -44,7 +44,9 @@ if (params.astrocyte) {
} else {
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
}
if (params.kitVersion == "3GEXv1") {
if (params.kitVersion == "3GEX") {
params.chemistryParam ='threeprime'
} else if (params.kitVersion == "3GEXv1") {
params.chemistryParam ='SC3Pv1'
} else if (params.kitVersion == "3GEXv2") {
params.chemistryParam ='SC3Pv2'
......@@ -52,6 +54,10 @@ if (params.astrocyte) {
params.chemistryParam ='SC3Pv3'
} else if (params.kitVersion == "5GEX") {
params.chemistryParam ='fiveprime'
} else if (params.kitVersion == "5GEXPE") {
params.chemistryParam ='SC5P-PE'
} else if (params.kitVersion == "5GEXR2") {
params.chemistryParam ='SC5P-R2'
} else {
params.chemistryParam = 'auto'
}
......
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