From 4e3398c6459b60daa62e5764879162930417a0b0 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 14 Aug 2020 12:42:38 -0500
Subject: [PATCH] Only run downstreamViz on param
---
astrocyte_pkg.yml | 11 +++++++++++
workflow/main.nf | 4 ++++
2 files changed, 15 insertions(+)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index 29f82cd..81b430f 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -159,6 +159,17 @@ workflow_parameters:
description: |
10x cellranger version.
+ - id: vizFiles
+ type: select
+ choices:
+ - [ 'true', 'Yes' ]
+ - [ 'false', 'No' ]
+ default: 'true'
+ required: true
+ description: |
+ Create objects which can be used for downstream visualization and analysis of each sample outputs. Currently created: Seurat R-objects.
+
+
- id: astrocyte
type: select
choices:
diff --git a/workflow/main.nf b/workflow/main.nf
index 7af1756..1fb8fca 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -81,6 +81,7 @@ expectCells = params.expectCells
forceCells = params.forceCells
chemistryParam = params.chemistryParam
version = params.version
+vizFiles = params.vizFiles
outDir = params.outDir
// Define script files
@@ -397,6 +398,9 @@ process downstreamViz {
file "*.rds" into seuratPaths
file "version_seurat.txt" into version_seurat
+ when:
+ vizFiles
+
script:
"""
hostname
--
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