From 3240eff6c3a200cf1bb04b144f1dac62a60c9b21 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 13 Apr 2020 10:26:59 -0500
Subject: [PATCH] Add 5prime chemistry option
---
astrocyte_pkg.yml | 7 ++++---
cleanup.sh | 7 +++++++
workflow/main.nf | 10 ++++++----
3 files changed, 17 insertions(+), 7 deletions(-)
create mode 100644 cleanup.sh
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 1a7cb7a..ff1a7c8 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -135,9 +135,10 @@ workflow_parameters:
type: select
default: 'auto'
choices:
- - ['auto', 'Auto Detect']
- - ['three', '3']
- - ['two', '2']
+ - ['auto', "Auto Detect"]
+ - ['3GEXv3', "3'GEX v3 (3' Gene Expression)"]
+ - ['3GEXv2', "3'GEX v2 (3' Gene Expression)"]
+ - ['5GEX', "5'GEX Auto (5' Gene Expression)"]
required: true
description: |
10x single cell gene expression chemistry version (only used in cellranger version 3.x).
diff --git a/cleanup.sh b/cleanup.sh
new file mode 100644
index 0000000..9569ff5
--- /dev/null
+++ b/cleanup.sh
@@ -0,0 +1,7 @@
+rm *.out
+rm pipeline_trace*.txt*
+rm report*.html*
+rm timeline*.html*
+rm .nextflow*.log*
+rm -r .nextflow/
+rm -r work/
diff --git a/workflow/main.nf b/workflow/main.nf
index f5cdf75..07b742e 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -31,12 +31,14 @@ if (params.kitVersion == "three" && params.version == '2.1.1') {
if (params.astrocyte) {
print("Running under astrocyte")
params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
- if (params.kitVersion == "one") {
+ if (params.kitVersion == "3GEXv1") {
params.chemistryParam ='SC3Pv1'
- } else if (params.kitVersion == "two") {
+ } else if (params.kitVersion == "3GEXv2") {
params.chemistryParam ='SC3Pv2'
- } else if (params.kitVersion == "three") {
+ } else if (params.kitVersion == "3GEXv3") {
params.chemistryParam ='SC3Pv3'
+ } else if (params.kitVersion == "5GEX") {
+ params.chemistryParam ='fiveprime'
} else {
params.chemistryParam = 'auto'
}
@@ -358,4 +360,4 @@ process multiqc {
multiqc -c ${multiqcConf} .
"""
-}
\ No newline at end of file
+}
--
GitLab