From d65e96f9f46d11981c94de997e962dbe8cfcf106 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Sat, 1 Sep 2018 14:31:59 -0500
Subject: [PATCH] Fix force-cells
---
astrocyte_pkg.yml | 2 +-
workflow/main.nf | 6 +++---
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/astrocyte_pkg.yml b/astrocyte_pkg.yml
index abc5772..dfd4015 100755
--- a/astrocyte_pkg.yml
+++ b/astrocyte_pkg.yml
@@ -120,7 +120,7 @@ workflow_parameters:
max: 10000
required: false
description: |
- Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option.
+ Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells.
# -----------------------------------------------------------------------------
# SHINY APP CONFIGURATION
diff --git a/workflow/main.nf b/workflow/main.nf
index dbd69e8..a0bcf3f 100755
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -81,13 +81,13 @@ process count {
"""
module load cellranger/2.1.1
"""
- if ( forceCells ==0){
+ if (forceCells == 0){
"""
cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
"""
} else {
"""
- cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells --force-cells=$forceCells
+ cellranger count --id="$sample" --transcriptome="$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
"""
}
-}
\ No newline at end of file
+}
--
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