From eae028c188b0fae8164eab90e41a7f8e21966066 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 11 Mar 2019 15:24:07 -0500
Subject: [PATCH] Put config params into main.nf for astrocyte
---
astrocyte_pkg.yml | 6 ++++++
workflow/main.nf | 29 ++++++++++++++++++++++++-----
2 files changed, 30 insertions(+), 5 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 4ccb571..4f0a76b 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -150,6 +150,12 @@ workflow_parameters:
description: |
10x cellranger version.
+ - id: astrocyte
+ type: select
+ default: 'true'
+ regex: 'true'
+ description: |
+ 10x cellranger version.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
diff --git a/workflow/main.nf b/workflow/main.nf
index df7ce2a..0c39a44 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -7,17 +7,36 @@
params.fastq = "$baseDir/../test_data/*.fastq.gz"
params.designFile = "$baseDir/../test_data/design.csv"
params.genome = 'GRCh38-3.0.0'
-params.genomes = []
-params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
-params.genomeLocationFull = params.genomeLocation+params.genome
+
+
params.expectCells = 10000
params.forceCells = 0
params.kitVersion = 'three'
-params.chemistry = []
-params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
+
params.version = '3.0.2'
+params.astrocyte = 'false'
params.outDir = "$baseDir/output"
+// Assign variables if astrocyte
+if (params.astrocyte == 'false') {
+ params.genomes = []
+ params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
+ params.chemistry = []
+ params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
+} else if (params.astrocyte == 'true') {
+ params.genomeLocation = '/project/apps_database/cellranger/refdata-cellranger-'
+ if (params.kitVersion == "one") {
+ params.chemistryParam ='SC3Pv1'
+ } else if (params.kitVersion == "two") {
+ params.chemistryParam ='SC3Pv2'
+ } else if (params.kitVersion == "three") {
+ params.chemistryParam ='SC3Pv3'
+ } else {
+ params.chemistryParam = "auto'
+ }
+}
+params.genomeLocationFull = params.genomeLocation+params.genome
+
// Define regular variables
designLocation = Channel
.fromPath(params.designFile)
--
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